Generative models have recently advanced de novo protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce RigidSSL (Rigidity-Aware Self-Supervised Learning), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.

Visual generation is increasingly ubiquitous in diverse domains, from text-to-image/video synthesis to multimodal interactive creation. Yet prevailing monolithic models remain fundamentally constrained by their inability to learn cumulatively and evolve autonomously, which is a limitation we term the "perpetual novice" problem. They lack mechanisms for structuring experience into reusable knowledge and therefore rely on brittle, "from-scratch" reasoning for each task, resulting in poor compositional generalization and inefficient knowledge retention. Motivated by these limitations, we propose SymbOmni, an agentic omni-model designed for cumulative evolution through Symbolic Concept Learning. At its core is the Symbolic Concept Box, an optimizable memory module that abstracts low-level operations into reusable Symbolic Workflow Instructions. SymbOmni operates through an induction-transduction cycle: experiences are abstracted into symbolic concepts (induction), which are then adaptively composed to solve novel tasks (transduction). The training is done by verbalized backpropagation with language-based feedback to enable continuous self-improvement without gradient-based model fine-tuning. Comprehensive experiments validate that (I) SymbOmni significantly outperforms existing agent-based systems for iterative creation and also surpasses closed-source models (e.g., Nano Banana, GPT-Image-1) in both image quality and task success rates; (II) SymbOmni effectively reduces token consumption by over 40

High-fidelity image generation faces a trade-off between speed and quality. Diffusion models produce strong visuals but require costly iterative sampling. Existing efficient methods mainly distill pretrained models into few-step samplers, a challenging process that depends heavily on teacher-model quality. In this paper, we introduce XYZFlow, a framework that rethinks efficient generation through multidimensional scaling of flow matching. Unlike single-step mappings, XYZFlow enhances expressivity by making probability paths more identifiable and learnable through structured multidimensional conditioning. We view autoregressive modeling as implicit flow straightening, where richer context reduces trajectory ambiguity. XYZFlow realizes this idea through two orthogonal dimensions: temporal scaling, which uses non-Markovian conditioning on the full denoising history; and spatial scaling, enabled by Next Shortcut Prediction, which sequentially generates patches using preceding patches' denoising trajectories as priors. Experiments show that XYZFlow achieves state-of-the-art performance, with 7.2-8.5X teacher speedups and competitive FID, while Next Shortcut Prediction delivers superior quality-latency trade-offs over model scaling or step reduction.

While low-rank adaptation (LoRA) is widely used for parameter-efficient model adaptation, how to regularize its training dynamics for stable and effective optimization remains underexplored. Because LoRA initializes the up-projection to zero, its early optimization dynamics are largely governed by the down-projection. Building on this observation, we introduce Normalized Low-Rank Adaptation (NoRA), a simple yet effective method that normalizes the down-projection matrices during training. We further show that the same normalization can be applied only at initialization, improving standard LoRA without requiring repeated normalization throughout training. Across pretraining, supervised finetuning, and reinforcement learning, NoRA consistently accelerates convergence, improves performance and training stability, and mitigates catastrophic forgetting. These benefits require neither additional trainable parameters nor inference-time computation, making NoRA a simple and broadly applicable enhancement to LoRA.

Muon has recently demonstrated strong empirical performance in large language model training, but the theoretical role of momentum in Muon remains unclear. Existing analyses of Muon either remove momentum to study spectral updates in isolation, or retain momentum without explaining why it improves empirical performance. Our work bridges this gap by showing momentum in Muon acts as a spectral filter. Under a structured signal-plus-perturbation gradient model, we prove that momentum suppresses perturbations while preserving the dominant signal, thereby enlarging the spectral gap between them. This enlarged gap stabilizes the singular subspaces of the matrix passed to Muon's orthogonalization step, making the resulting update more reliable. We further show that applying momentum before orthogonalization achieves provably stronger alignment with the signal component of the gradient than either reversing this order or simply removing momentum. Experiments across diverse tasks, including LLM pretraining, support our theoretical analysis. More broadly, our theory offers a starting point for understanding the benefits of momentum in other matrix-based optimizers.

Superconducting quantum computing is one of the most mature solid-state platforms for quantum computation, with processors exceeding one hundred qubits. Yet further scaling toward fault-tolerant quantum computing is increasingly constrained by calibration complexity. Conventional scripts are brittle to anomalous signals, and expert judgment is bounded by cognitive bandwidth and serial operation time, failing to keep pace with system scale. Here we report Vibe Calibration, an autonomous calibration system orchestrated by large language model agents, which distills expert tacit knowledge into reusable Skills. Each Skill is organized as a decision tree that packages parameterized measurement commands, quantitative acceptance criteria, and audit records, enabling autonomous execution and self-healing. We capture this knowledge through a three-phase human-in-the-loop distillation process and fine-tune a large language model on validated trajectories. On a 112-qubit processor with frequency-tunable transmons, the system autonomously completes calibration of 108 out of 112 qubits in 4.7 hours, achieving a 4–5× speedup over manual calibration of the full 112 qubits. A cross-validated comparison with expert manual calibration on a 16-qubit subset shows agreement on 14 out of 16 qubits. More importantly, the model demonstrates transferable calibration workflows across devices. While low-level control scripts require minor interface adaptation for different hardware platforms, the core decision logic and task orchestration generalize to new processors, demonstrating a reusable laboratory interface rather than a memorized script.This work demonstrates, for the first time, fully autonomous calibration of a hundred-qubit superconducting processor through reusable and auditable Skills, removing a critical barrier to scalable quantum hardware operation.

Muon has recently emerged as a competitive alternative to AdamW for large-scale pre-training, with orthogonalization via Newton-Schulz (NS) iterations as its core operation. Existing Muon variants apply a uniform NS schedule to all parameter matrices, overlooking possible differences in orthogonalization difficulty and its impact on performance. Through a systematic empirical study, we show that this per-matrix heterogeneity is pervasive and largely determined by matrix geometry, which evolves dynamically across operator types, training stages, and network depths. As a result, uniform NS schedules can lead to uneven orthogonalization quality across the model. Motivated by these findings, we propose Adaptive Muon Orthogonalization (AMO), an observe-then-commit method that measures weight geometry by operator type early in training and then uses these signals to allocate the NS budget for the remainder of training. AMO delivers consistent improvements over uniform-schedule Muon across standard, prolonged, and continual pre-training, surpassing the strongest baseline by +0.76 on Llama3.1-1.4B and +0.51 on Qwen3-1.7B in average downstream performance of 12 evaluation tasks.

Adapting CLIP to vertical domains is typically approached by novel fine-tuning strategies or by scaling up domain-specific datasets. We revisit this task from a data-centric perspective: {Can effective data selection substitute for large-scale datasets in continual pre-training (CPT)?} We introduce \textbf{CHIPS} (\textbf{C}urvature-aware \textbf{H}ybrid \textbf{I}nfluence in \textbf{P}rojection \textbf{S}ubspace), which assigns each image–text pair a utility that integrates three complementary factors aligned with three goals: \textit{faithfulness} via a curvature-aware, Newton-style alignment computed in CLIP’s end-point subspace; \textit{scalability} via an InfoNCE-aware curvature estimator with Johnson–Lindenstrauss (JL) sketching; and \textit{retention} via a selection-aware relevance weight combined with learnability to balance target adaptation against general-domain preservation. We justify this design theoretically by proving a lower‑bound guarantee on the proxy’s correlation with full‑parameter alignment and by characterizing the bias–variance trade‑offs introduced by curvature mixing and JL sketching.We evaluate CHIPS empirically across various settings: 1) CHIPS attains state-of-the-art performance among selection baselines on 17 \textbf{medical benchmarks}, matches full-dataset CPT with 30\% of the data, and outperforms half-dataset CPT using only 10\%; 2) on 31 \textbf{general-domain benchmarks}, CHIPS yields the smallest performance drop under 10--30\% data-retention budgets. Code, data, and model checkpoints will be released.

Parameter-efficient finetuning (PEFT) has become the standard approach for adapting large language models, yet evaluations largely emphasize downstream accuracy while overlooking the retention of pretrained capabilities. We argue that PEFT should be assessed through the stability-plasticity dilemma: the trade-off between target-task adaptation and resistance to forgetting. We introduce PEFT-Arena, a benchmark that jointly measures downstream performance and general capability retention. Across methods, we find distinct stability-plasticity profiles; under comparable parameter budgets, orthogonal finetuning achieves the most favorable Pareto frontier. To explain these differences, we analyze PEFT updates from two geometric perspectives. In weight space, spectral analysis reveals how parameterizations interact with the pretrained singular-value structure. In activation space, retention metrics show whether finetuning preserves or distorts general-capability representations, with forgetting linked to non-isometric representation distortion. Finally, an analysis shows that final SFT checkpoints often overshoot a better target-retention operating point. Inspired by this, we present case studies of a post-hoc improvement with path-wise rewinding.

LLM-based LEGO assembly generation requires both semantic grounding and physical feasibility. We identify a data-induced failure mode, PhysHack, in which the assemblies satisfy physical-validity constraints while producing structures that are geometrically misaligned, semantically inconsistent, or poorly calibrated. To address this challenge, we propose a model-based data selection approach that uses only a small fraction of the training data while improving physically grounded LEGO assembly generation. Building on the selected trajectories, we introduce PVPO, a sample-efficient reinforcement learning method that couples physical feasibility with voxel-space geometric rewards. Our results show that physical validity alone is an insufficient proxy for reliable physical reasoning: models can learn to generate valid structures without preserving semantic or geometric fidelity. Experiments across model backbones and test-time scaling settings demonstrate that PVPO improves structural and semantic alignment, physical validity, structural stability, and calibration, while reducing reliance on extensive post-hoc rejection sampling. In particular, results on calibration show that PVPO mitigates PhysHack by making test-time selection more predictive of semantic and structural quality.

Curriculum learning (CL), motivated by the intuition that learning in increasing order of difficulty should ease generalization, is commonly adopted both in pre-training and post-training of large language models (LLMs). The intuition of CL is particularly compelling for compositional reasoning, where complex problems are built from elementary inference rules; however, the actual impact of CL on such tasks remains largely underexplored. We present a systematic empirical study of CL for post-training of LLMs, using synthetic arithmetic and logical benchmarks where difficulty is characterized by reasoning complexity rather than surface-level proxies. Surprisingly, across multiple model families and curriculum schedules, we find no robust advantage in difficulty-based sequencing over standard random sampling in either accuracy or response length. These findings persist across both supervised fine-tuning (SFT) and reinforcement learning (RL) methods. Our study suggests that, in the context of deductive reasoning, the specific ordering of training examples plays a negligible role in achieving compositional generalization, challenging the practical utility of curriculum-based post-training.

Efficient and stable training of large language models (LLMs) remains a core challenge in modern machine learning systems. We tackle this problem with Reparameterized Orthogonal Equivalence Training (POET), a spectrum-preserving framework that optimizes each weight matrix through orthogonal equivalence transformation. Although POET provides strong training stability, its original implementation incurs high memory consumption and computational overhead due to intensive matrix multiplications. To overcome these limitations, we introduce POET-X, a scalable and memory-efficient variant that performs orthogonal equivalence transformations with significantly reduced computational cost. POET-X maintains the generalization and stability benefits of POET while achieving substantial improvements in throughput and memory efficiency. In experiments, POET-X enables the pretraining of billion-parameter LLMs on a single Nvidia H100 GPU, and in contrast, standard optimizers such as AdamW run out of memory under the same settings.

Large-scale pretrained diffusion models have significantly enhanced the quality of generated videos, and yet their use in real-time streaming remains limited. Autoregressive models offer a natural framework for sequential frame synthesis but require heavy computation to achieve high fidelity. Diffusion distillation can compress these models into efficient few-step variants, but existing video distillation approaches largely adapt image-specific methods that neglect temporal dependencies. These techniques often excel in image generation but underperform in video synthesis, exhibiting reduced motion coherence, error accumulation over long sequences, and a latency–quality trade-off. We identify two factors that result in these limitations: insufficient utilization of temporal context during step reduction and implicit prediction of subsequent noise levels in next-chunk prediction (exposure bias). To address these issues, we propose Diagonal Distillation, which operates orthogonally to existing approaches and better exploits temporal information across both video chunks and denoising steps. Central to our approach is an asymmetric generation strategy: more steps early, fewer steps later. This design allows later chunks to inherit rich appearance information from thoroughly processed early chunks, while using partially denoised chunks as conditional inputs for subsequent synthesis. By aligning the implicit prediction of subsequent noise levels during chunk generation with the actual inference conditions, our approach mitigates error propagation and reduces oversaturation in long-range sequences. We further incorporate implicit optical flow modeling to preserve motion quality under strict step constraints. Our method generates a 5-second video in just 2.61 seconds (up to 31 FPS), achieving a 277.3× speedup over the undistilled model and doubling the acceleration ratio of the state-of-the-art (140×) without sacrificing visual quality. The source code and trained models will be released and we have uploaded the video to an anonymous hosting service at: https://diagonal-distillation.github.io/.

Protein design stands as one of biology’s most important frontiers, with the potential to transform medicine, advance human health, and drive sustainability. Protein generation, a central task in protein design, has been greatly accelerated by AI-driven models—such as FoldFlow, MultiFlow, and AlphaFlow that build on residue-wise rigidity–based modeling pioneered by AlphaFold2. Residue-wise rigid-body representations reduce structural dimensionality while enforcing chemical constraints, enabling more efficient and physically consistent protein structure generation than all-atom modeling. Despite these advances, existing models often underutilize the vast structural information available in large-scale protein datasets. This highlights the importance of pretraining, which can provide richer representations and improve generalization across diverse protein design tasks. More importantly, the challenge lies in how to fully exploit abundant, low-cost unlabeled protein datasets using unsupervised pretraining. We introduce RigidSSL, a rigidity-based pretraining framework for proteins. RigidSSL canonicalizes structures into an inertial frame, employs a two-phase workflow combining large-scale perturbations and molecular dynamics views, and applies a rigid-body flow matching objective with Invariant Point Attention to capture global geometry. This enables learning stable, geometry-aware representations that improve downstream protein generation. To evaluate the effectiveness of RigidSSL, we conduct quantitative experiments on the protein generation task. Empirically, RigidSSL outperforms previous state-of-the-art geometric pretraining algorithms, leading to improvements in unconditional generation across all metrics, including designability, novelty, and diversity, for length up to 800 residues.

We introduce Pion, a spectrum-preserving optimizer for large language model (LLM) training based on orthogonal equivalence transformation. Unlike additive optimizers such as Adam and Muon, Pion updates each weight matrix through left and right orthogonal transformations, preserving its singular values throughout training. This yields an optimization mechanism that modulates the geometry of weight matrices while keeping their spectral norm fixed. We derive the Pion update rule, systematically examine its design choices, and analyze its convergence behavior along with several key properties. Empirical results show that Pion offers a stable and competitive alternative to standard optimizers for both LLM pretraining and finetuning.

Solving complex planning problems requires Large Language Models (LLMs) to explicitly model the state transition to avoid rule violations, comply with constraints, and ensure optimality-a task hindered by the inherent ambiguity of natural language. To overcome such ambiguity, Planning Domain Definition Language (PDDL) is leveraged as a planning abstraction that enables precise and formal state descriptions. With PDDL, we can generate a symbolic world model where classic searching algorithms, such as A*, can be seamlessly applied to find optimal plans. However, directly generating PDDL domains with current LLMs remains an open challenge due to the lack of PDDL training data. To address this challenge, we propose to scale up the test-time computation of LLMs to enhance their PDDL reasoning capabilities, thereby enabling the generation of high-quality PDDL domains. Specifically, we introduce a simple yet effective algorithm, which first employs a Best-of-N sampling approach to improve the quality of the initial solution and then refines the solution in a fine-grained manner with verbalized machine learning. Our method outperforms o1-mini by a considerable margin in the generation of PDDL domain, achieving over 50 success rate on two tasks (i.e., generating PDDL domains from natural language description or PDDL problems). This is done without requiring additional training. By taking advantage of PDDL as state abstraction, our method is able to outperform current state-of-the-art methods on almost all competition-level planning tasks.

Orthogonal finetuning (OFT) offers highly parameter-efficient adaptation while preventing catastrophic forgetting, but its high runtime and memory demands limit practical deployment. We identify the core computational bottleneck in OFT as its weight-centric implementation, which relies on costly matrix-matrix multiplications with cubic complexity. To overcome this, we propose OFTv2, an input-centric reformulation that instead uses matrix-vector multiplications (i.e., matrix-free computation), reducing the computational cost to quadratic. We further introduce the Cayley-Neumann parameterization, an efficient orthogonal parameterization that approximates the matrix inversion in Cayley transform via a truncated Neumann series. These modifications allow OFTv2 to achieve up to 10x faster training and 3x lower GPU memory usage without compromising performance. In addition, we extend OFTv2 to support finetuning quantized foundation models and show that it outperforms the popular QLoRA in training stability, efficiency, and memory usage.

Model merging is an efficient post-training strategy for integrating knowledge from multiple finetuned checkpoints of a shared foundation model. Existing methods operate in the parameter space, combining task vectors to mitigate conflicts, but remain constrained by parameter inconsistencies. We propose Functional Dual Anchors (FDAs), a framework that instead models the input-representation space. FDAs are synthetic inputs whose induced gradients align with task vectors, capturing task-specific functional shifts relative to the pretrained model. This perspective bridges joint multi-task training and post-hoc merging, offering both robustness and flexibility. We further introduce a principled initialization scheme and show that FDAs are complementary to parameter-space model merging. Comprehensive experiments demonstrate the effectiveness of FDAs in model merging.

We revisit the likelihood ratio between a pretrained large language model (LLM) and its finetuned variant as a criterion for out-of-distribution (OOD) detection. The intuition behind such a criterion is that, the pretrained LLM has the prior knowledge about OOD data due to its large amount of training data, and once finetuned with the in-distribution data, the LLM has sufficient knowledge to distinguish their difference. Leveraging the power of LLMs, we show that, the likelihood ratio can serve as an effective OOD detection criterion. Moreover, we apply the proposed LLM-based likelihood ratio to detect OOD questions in question-answering (QA) systems, which can be used to improve the performance of specialized LLMs for general questions. Given that likelihood can be easily obtained by the loss functions within contemporary neural network frameworks, it is straightforward to implement this approach in practice with three lines of code. Since both the pretrained LLMs and its various finetuned models are widely available from online platforms such as Hugging Face, our proposed criterion can be effortlessly incorporated for OOD detection without the need for further training. We conduct comprehensive evaluation across on multiple settings, including far OOD, near OOD, Spam detection, and QA scenarios, to demonstrate the effectiveness of the method. Code can be found at https://github.com/andiac/LLMOODratio

Large Language Models (LLMs) have exhibited exceptional performance across a spectrum of natural language processing tasks. However, their substantial sizes pose considerable challenges, particularly in computational demands and inference speed, due to their quadratic complexity. In this work, we have identified a key pattern: certain seemingly meaningless separator tokens (i.e., punctuations) contribute disproportionately to attention scores compared to semantically meaningful tokens. This observation suggests that information of the segments between these separator tokens can be effectively condensed into the separator tokens themselves without significant information loss. Guided by this insight, we introduce SepLLM, a plug-and-play framework that accelerates inference by compressing these segments and eliminating redundant tokens. Additionally, we implement efficient kernels for training acceleration. Experimental results across training-free, training-from-scratch, and post-training settings demonstrate SepLLM's effectiveness. Notably, using the Llama-3-8B backbone, SepLLM achieves over 50% reduction in KV cache on the GSM8K-CoT benchmark while maintaining comparable performance. Furthermore, in streaming settings, SepLLM effectively processes sequences of up to 4 million tokens or more while maintaining consistent language modeling capabilities.