Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation

Many generative tasks in chemistry and science involve distributions invariant to group symmetries (e.g., permutation and rotation). A common strategy enforces invariance and equivariance through architectural constraints such as equivariant denoisers and invariant priors. In this paper, we challenge this tradition through the alternative canonicalization perspective: first map each sample to an orbit representative with a canonical pose or order, train an unconstrained (non-equivariant) diffusion or flow model on the canonical slice, and finally recover the invariant distribution by sampling a random symmetry transform at generation time. Building on a formal quotient-space perspective, our work provides a comprehensive theory of canonical diffusion by proving: (i) the correctness, universality and superior expressivity of canonical generative models over invariant targets; (ii) canonicalization accelerates training by removing diffusion score complexity induced by group mixtures and reducing conditional variance in flow matching. We then show that aligned priors and optimal transport act complementarily with canonicalization and further improves training efficiency. We instantiate the framework for molecular graph generation under $S_n \times SE(3)$ symmetries. By leveraging geometric spectra-based canonicalization and mild positional encodings, canonical diffusion significantly outperforms equivariant baselines in 3D molecule generation tasks, with similar or even less computation. Moreover, with a novel architecture Canon, CanonFlow achieves state-of-the-art performance on the challenging GEOM-DRUG dataset, and the advantage remains large in few-step generation.

GREPO: A Benchmark for Graph Neural Networks on Repository-Level Bug Localization

Repository-level bug localization-the task of identifying where code must be modified to fix a bug-is a critical software engineering challenge. Standard Large Language Modles (LLMs) are often unsuitable for this task due to context window limitations that prevent them from processing entire code repositories. As a result, various retrieval methods are commonly used, including keyword matching, text similarity, and simple graph-based heuristics such as Breadth-First Search. Graph Neural Networks (GNNs) offer a promising alternative due to their ability to model complex, repository-wide dependencies; however, their application has been hindered by the lack of a dedicated benchmark. To address this gap, we introduce GREPO, the first GNN benchmark for repository-scale bug localization tasks. GREPO comprises 86 Python repositories and 47294 bug-fixing tasks, providing graph-based data structures ready for direct GNN processing. Our evaluation of various GNN architectures shows outstanding performance compared to established information retrieval baselines. This work highlights the potential of GNNs for bug localization and established GREPO as a foundation resource for future research, The code is available at https://github.com/qingpingmo/GREPO.

SHINE: A Scalable In-Context Hypernetwork for Mapping Context to LoRA in a Single Pass

We propose SHINE (Scalable Hyper In-context NEtwork), a scalable hypernetwork that can map diverse meaningful contexts into high-quality LoRA adapters for large language models (LLM). By reusing the frozen LLM's own parameters in an in-context hypernetwork design and introducing architectural innovations, SHINE overcomes key limitations of prior hypernetworks and achieves strong expressive power with a relatively small number of parameters. We introduce a pretraining and instruction fine-tuning pipeline, and train our hypernetwork to generate high quality LoRA adapters from diverse meaningful contexts in a single forward pass. It updates LLM parameters without any fine-tuning, and immediately enables complex question answering tasks related to the context without directly accessing the context, effectively transforming in-context knowledge to in-parameter knowledge in one pass. Our work achieves outstanding results on various tasks, greatly saves time, computation and memory costs compared to SFT-based LLM adaptation, and shows great potential for scaling. Our code is available at https://github.com/Yewei-Liu/SHINE

LiteToken: Removing Intermediate Merge Residues From BPE Tokenizers

Tokenization is fundamental to how language models represent and process text, yet the behavior of widely used BPE tokenizers has received far less study than model architectures and training. In this paper, we investigate intermediate merge residues in BPE vocabularies: tokens that are frequent during merge learning so that retained in the final vocabulary, but are mostly further merged and rarely emitted when tokenizing the corpus during tokenizer usage. Such low-frequency tokens not only waste vocabulary capacity but also increase vulnerability to adversarial or atypical inputs. We present a systematic empirical characterization of this phenomenon across commonly used tokenizers and introduce LiteToken, a simple method for removing residue tokens. Because the affected tokens are rarely used, pretrained models can often accommodate the modified tokenizer without additional fine-tuning. Experiments show that LiteToken reduces token fragmentation, reduces parameters, and improves robustness to noisy or misspelled inputs, while preserving overall performance.

Proof-RM: A Scalable and Generalizable Reward Model for Math Proof

While Large Language Models (LLMs) have demonstrated strong math reasoning abilities through Reinforcement Learning with *Verifiable Rewards* (RLVR), many advanced mathematical problems are proof-based, with no guaranteed way to determine the authenticity of a proof by simple answer matching. To enable automatic verification, a Reward Model (RM) capable of reliably evaluating full proof processes is required. In this work, we design a *scalable* data-construction pipeline that, with minimal human effort, leverages LLMs to generate a large quantity of high-quality "**question-proof-check**" triplet data. By systematically varying problem sources, generation methods, and model configurations, we create diverse problem-proof pairs spanning multiple difficulty levels, linguistic styles, and error types, subsequently filtered through hierarchical human review for label alignment. Utilizing these data, we train a proof-checking RM, incorporating additional process reward and token weight balance to stabilize the RL process. Our experiments validate the model's scalability and strong performance from multiple perspectives, including reward accuracy, generalization ability and test-time guidance, providing important practical recipes and tools for strengthening LLM mathematical capabilities.

Breaking the Blocks: Continuous Low-Rank Decomposed Scaling for Unified LLM Quantization and Adaptation

Current quantization methods for LLMs predominantly rely on block-wise structures to maintain efficiency, often at the cost of representational flexibility. In this work, we demonstrate that element-wise quantization can be made as efficient as block-wise scaling while providing strictly superior expressive power by modeling the scaling manifold as continuous low-rank matrices ($S = BA$). We propose Low-Rank Decomposed Scaling (LoRDS), a unified framework that rethinks quantization granularity through this low-rank decomposition. By "breaking the blocks" of spatial constraints, LoRDS establishes a seamless efficiency lifecycle: it provides high-fidelity PTQ initialization refined via iterative optimization, enables joint QAT of weights and scaling factors, and facilitates high-rank multiplicative PEFT adaptation. Unlike additive PEFT approaches such as QLoRA, LoRDS enables high-rank weight updates within a low-rank budget while incurring no additional inference overhead. Supported by highly optimized Triton kernels, LoRDS consistently outperforms state-of-the-art baselines across various model families in both quantization and downstream fine-tuning tasks. Notably, on Llama3-8B, our method achieves up to a 27.0% accuracy improvement at 3 bits over NormalFloat quantization and delivers a 1.5x inference speedup on NVIDIA RTX 4090 while enhancing PEFT performance by 9.6% on downstream tasks over 4bit QLoRA, offering a robust and integrated solution for unified compression and adaptation of LLMs.

Knowledge is Not Enough: Injecting RL Skills for Continual Adaptation

Large Language Models (LLMs) face the "knowledge cutoff" challenge, where their frozen parametric memory prevents direct internalization of new information. While Supervised Fine-Tuning (SFT) is commonly used to update model knowledge, it often updates factual content without reliably improving the model's ability to use the newly incorporated information for question answering or decision-making. Reinforcement Learning (RL) is essential for acquiring reasoning skills; however, its high computational cost makes it impractical for efficient online adaptation. We empirically observe that the parameter updates induced by SFT and RL are nearly orthogonal. Based on this observation, we propose Parametric Skill Transfer (PaST), a framework that supports modular skill transfer for efficient and effective knowledge adaptation. By extracting a domain-agnostic Skill Vector from a source domain, we can linearly inject knowledge manipulation skills into a target model after it has undergone lightweight SFT on new data. Experiments on knowledge-incorporation QA (SQuAD, LooGLE) and agentic tool-use benchmarks (ToolBench) demonstrate the effectiveness of our method. On SQuAD, PaST outperforms the state-of-the-art self-editing SFT baseline by up to 9.9 points. PaST further scales to long-context QA on LooGLE with an 8.0-point absolute accuracy gain, and improves zero-shot ToolBench success rates by +10.3 points on average with consistent gains across tool categories, indicating strong scalability and cross-domain transferability of the Skill Vector.

SubTokenTest: A Practical Benchmark for Real-World Sub-token Understanding

Recent advancements in large language models (LLMs) have significantly enhanced their reasoning capabilities. However, they continue to struggle with basic character-level tasks, such as counting letters in words, a problem rooted in their tokenization process. While existing benchmarks have highlighted this weakness through basic character operations, such failures are often dismissed due to lacking practical relevance. Yet, many real-world applications, such as navigating text-based maps or interpreting structured tables, rely heavily on precise sub-token understanding. In this regard, we introduce SubTokenTest, a comprehensive benchmark that assesses sub-token understanding through practical, utility-driven tasks. Our benchmark includes ten tasks across four domains and isolates tokenization-related failures by decoupling performance from complex reasoning. We provide a comprehensive evaluation of nine advanced LLMs. Additionally, we investigate the impact of test-time scaling on sub-token reasoning and explore how character-level information is encoded within the hidden states.

What Affects the Effective Depth of Large Language Models?

The scaling of large language models (LLMs) emphasizes increasing depth, yet performance gains diminish with added layers. Prior work introduces the concept of "effective depth", arguing that deeper models fail to fully utilize their layers for meaningful computation. Building on this, we systematically study how effective depth varies with model scale, training type, and task difficulty. First, we analyze the model behavior of Qwen-2.5 family (1.5B-32B) and find that while the number of effective layers grows with model size, the effective depth ratio remains stable. Besides, comparisons between base and corresponding long-CoT models show no increase in effective depth, suggesting that improved reasoning stems from longer context rather than deeper per-token computation. Furthermore, evaluations across tasks of varying difficulty indicate that models do not dynamically use more layers for harder problems. Our results suggest that current LLMs underuse available depth across scales, training paradigms and tasks of varying difficulties, pointing out research opportunities on increasing the layer utilization rate of LLMs, model pruning, and early exiting. Our code is released at https://github.com/AheadOFpotato/what_affects_effective_depth.

Diffusion As Self-Distillation: End-to-End Latent Diffusion In One Model

Standard Latent Diffusion Models rely on a complex, three-part architecture consisting of a separate encoder, decoder, and diffusion network, which are trained in multiple stages. This modular design is computationally inefficient, leads to suboptimal performance, and prevents the unification of diffusion with the single-network architectures common in vision foundation models. Our goal is to unify these three components into a single, end-to-end trainable network. We first demonstrate that a naive joint training approach fails catastrophically due to ``latent collapse'', where the diffusion training objective interferes with the network's ability to learn a good latent representation. We identify the root causes of this instability by drawing a novel analogy between diffusion and self-distillation based unsupervised learning method. Based on this insight, we propose Diffusion as Self-Distillation (DSD), a new framework with key modifications to the training objective that stabilize the latent space. This approach enables, for the first time, the stable end-to-end training of a single network that simultaneously learns to encode, decode, and perform diffusion. DSD achieves outstanding performance on the ImageNet $256\times 256$ conditional generation task: FID=13.44/6.38/4.25 with only 42M/118M/205M parameters and 50 training epochs on ImageNet, without using classifier-free-guidance.