Ruijun Huang

Xiangru Tang, Yuliang Liu, Zefan Cai et al. · pku

Despite Large Language Models (LLMs) like GPT-4 achieving impressive results in function-level code generation, they struggle with repository-scale code understanding (e.g., coming up with the right arguments for calling routines), requiring a deeper comprehension of complex file interactions. Also, recently, people have developed LLM agents that attempt to interact with repository code (e.g., compiling and evaluating its execution), prompting the need to evaluate their performance. These gaps have motivated our development of ML-Bench, a benchmark rooted in real-world programming applications that leverage existing code repositories to perform tasks. Addressing the need for LLMs to interpret long code contexts and translate instructions into precise, executable scripts, ML-Bench encompasses annotated 9,641 examples across 18 GitHub repositories, challenging LLMs to accommodate user-specified arguments and documentation intricacies effectively. To evaluate both LLMs and AI agents, two setups are employed: ML-LLM-Bench for assessing LLMs' text-to-code conversion within a predefined deployment environment, and ML-Agent-Bench for testing autonomous agents in an end-to-end task execution within a Linux sandbox environment. Our findings indicate that while GPT-4o leads with a Pass@5 rate surpassing 50%, there remains significant scope for improvement, highlighted by issues such as hallucinated outputs and difficulties with bash script generation. Notably, in the more demanding ML-Agent-Bench, GPT-4o achieves a 76.47% success rate, reflecting the efficacy of iterative action and feedback in complex task resolution. Our code, dataset, and models are available at https://github.com/gersteinlab/ML-bench.

Ruijun Huang, Zhiqiao Kang, Yuxuan Zhu et al.

The accurate extraction of scientific measurements from literature is a critical yet challenging task in AI4Science, enabling large-scale analysis and integration of quantitative research findings. However, Large Language Models (LLMs) frequently exhibit severe hallucinations, which significantly undermine the reliability of automated scientific document understanding systems. To address this problem, we propose MeasHalu, a novel framework for mitigating scientific measurement hallucinations through enhanced reasoning and targeted optimization. We first present a fine-grained taxonomy of measurement-specific hallucinations, categorizing errors across quantities, units, modifiers, and relations. Our approach incorporates a two-stage reasoning-aware fine-tuning strategy using augmented scientific data and process-based supervision. Furthermore, we introduce a progressive reward curriculum designed to penalize specific hallucination types, significantly improving extraction faithfulness. Experimental results demonstrate that MeasHalu substantially reduces hallucination rates and improves overall accuracy on the MeasEval benchmark. This work provides a targeted solution to a key bottleneck in automated scientific knowledge extraction, facilitating more trustworthy and scalable machine-assisted scientific literature analysis.

Anrui Chen, Ruijun Huang, Xin Zhang et al.

Mixture-of-Experts (MoE) architectures are often considered a natural fit for continual learning because sparse routing should localize updates and reduce interference, yet MoE Transformers still forget substantially even with sparse, well-balanced expert utilization. We attribute this gap to a pre-routing bottleneck: multi-head attention concatenates head-specific signals into a single post-attention router input, forcing routing to act on co-occurring feature compositions rather than separable head channels. We show that this router input simultaneously encodes multiple separately decodable semantic and structural factors with uneven head support, and that different feature compositions induce weakly aligned parameter-gradient directions; as a result, routing maps many distinct compositions to the same route. We quantify this collision effect via a route-wise effective composition number $N_{eff}$ and find that higher $N_{eff}$ is associated with larger old-task loss increases after continual training. Motivated by these findings, we propose MH-MoE, which performs head-wise routing over sub-representations to increase routing granularity and reduce composition collisions. On TRACE with Qwen3-0.6B/8B, MH-MoE effectively mitigates forgetting, reducing BWT on Qwen3-0.6B from 11.2% (LoRAMoE) to 4.5%.

Ruijun Huang, Fang Dong, Xin Zhang et al.

Mixture-of-Experts (MoE) architectures scale Large Language Models via expert specialization induced by conditional computation. In practice, however, expert specialization often fails: some experts become functionally similar, while others functioning as de facto shared experts, limiting the effective capacity and model performance. In this work, we analysis from a spectral perspective on parameter and gradient spaces, uncover that (1) experts share highly overlapping dominant spectral components in their parameters, (2) dominant gradient subspaces are strongly aligned across experts, driven by ubiquitous low-rank structure in human corpus, and (3) gating mechanisms preferentially route inputs along these dominant directions, further limiting specialization. To address this, we propose Spectral-Decoupled MoE (SD-MoE), which decomposes both parameter and gradient in the spectral space. SD-MoE improves performance across downstream tasks, enables effective expert specialization, incurring minimal additional computation, and can be seamlessly integrated into a wide range of existing MoE architectures, including Qwen and DeepSeek.

Zhendong Huang, Hengjie Cao, Fang Dong et al.

Gradient signals in LLM training are highly anisotropic: recurrent linguistic structure concentrates energy into a small set of dominant spectral directions, while context specific information resides in a long tail. We show that this spike tail separation persists throughout training, with the spike occupying only about 1.5% of directions yet dominating optimizer statistics. This dominance suppresses tail learning by contracting tail updates through second moment normalization and tightening the globally stable learning rate bound. Motivated by this analysis, we propose Spectra, a spike aware optimizer that suppresses the dominant low rank spike subspace without amplifying the noise sensitive spectral tail. Spectra tracks the spike subspace via cached, warm started power iteration and applies low rank spectral shaping with negligible overhead and substantially reduced optimizer state memory. On LLaMA3 8B trained on 50B tokens, Spectra reaches the same target loss 30% faster than AdamW, reduces per step end to end overhead by 0.7%, cuts optimizer state memory by 49.25%, and improves average downstream accuracy by 1.62%. Compared to Muon, Spectra is 5.1x faster in optimizer processing time, achieves a lower final loss, and improves average accuracy by 0.66%.

Hengjie Cao, Zhendong Huang, Mengyi Chen et al.

Large language models trained on natural language exhibit pronounced anisotropy: a small number of directions concentrate disproportionate energy, while the remaining dimensions form a broad semantic tail. In low-bit training regimes, this geometry becomes numerically unstable. Because blockwise quantization scales are determined by extreme elementwise magnitudes, dominant directions stretch the dynamic range, compressing long-tail semantic variation into narrow numerical bins. We show that this instability is primarily driven by a coherent rank-one mean bias, which constitutes the dominant component of spectral anisotropy in LLM representations. This mean component emerges systematically across layers and training stages and accounts for the majority of extreme activation magnitudes, making it the principal driver of dynamic-range inflation under low precision. Crucially, because the dominant instability is rank-one, it can be eliminated through a simple source-level mean-subtraction operation. This bias-centric conditioning recovers most of the stability benefits of SVD-based spectral methods while requiring only reduction operations and standard quantization kernels. Empirical results on FP4 (W4A4G4) training show that mean removal substantially narrows the loss gap to BF16 and restores downstream performance, providing a hardware-efficient path to stable low-bit LLM training.

Hengjie Cao, Mengyi Chen, Yifeng Yang et al.

This work investigates the optimization instability of deep neural networks from a less-explored yet insightful perspective: the emergence and amplification of singularities in the parametric space. Our analysis reveals that parametric singularities inevitably grow with gradient updates and further intensify alignment with representations, leading to increased singularities in the representation space. We show that the gradient Frobenius norms are bounded by the top singular values of the weight matrices, and as training progresses, the mutually reinforcing growth of weight and representation singularities, termed the curse of singularities, relaxes these bounds, escalating the risk of sharp loss explosions. To counter this, we propose Parametric Singularity Smoothing (PSS), a lightweight, flexible, and effective method for smoothing the singular spectra of weight matrices. Extensive experiments across diverse datasets, architectures, and optimizers demonstrate that PSS mitigates instability, restores trainability even after failure, and improves both training efficiency and generalization.

Hengjie Cao, Mengyi Chen, Yifeng Yang et al.

This work identifies anisotropy in the singular value spectra of parameters, activations, and gradients as the fundamental barrier to low-bit training of large language models (LLMs). These spectra are dominated by a small fraction of large singular values, inducing wide numerical ranges that cause quantization bias and severe spectral distortion, ultimately degrading training performance. This work presents Metis, a spectral-domain quantization framework that partitions anisotropic spectra into narrower sub-distributions for independent quantization, thereby reducing errors and preserving spectral structure. To minimize overhead, Metis leverages two key properties of the dominant spectral subspace: preservation via sparsely random sampling and preservation via random projection, reducing decomposition cost to a negligible level. On LLaMA-3 8B trained with 100B tokens, Metis enables robust W4A4G4 training with FP4 quantization of weights, activations, and gradients, yielding only a 0.4% training loss gap and a 0.1% degradation in downstream accuracy relative to BF16. Beyond matching BF16 fidelity, Metis also surpasses our implementation of Nvidia's recently announced (yet to be publicly released) FP4 recipe, consistently achieving lower loss and higher downstream accuracy while incurring significantly lower computational overhead. The code implementation for Metis is available at: https://anonymous.4open.science/r/Metis-quantization-644B.