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Ruizhe Chen

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10 papers

2 author rows

ICML Conference 2025 Conference Paper

An All-Atom Generative Model for Designing Protein Complexes

Ruizhe Chen
Dongyu Xue
Xiangxin Zhou
Zaixiang Zheng
Xiangxiang Zeng
Quanquan Gu

Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in models like the series of ESM and AlphaFold2. Despite these developments, the study and modeling of multi-chain proteins remain largely uncharted, though they are vital for understanding biological functions. Recognizing the importance of these interactions, we introduce APM (all-Atom Protein generative Model), a model specifically designed for modeling multi-chain proteins. By integrating atom-level information and leveraging data on multi-chain proteins, APM is capable of precisely modeling inter-chain interactions and designing protein complexes with binding capabilities from scratch. It also performs folding and inverse-folding tasks for multi-chain proteins. Moreover, APM demonstrates versatility in downstream applications: it achieves enhanced performance through supervised fine-tuning (SFT) while also supporting zero-shot sampling in certain tasks, achieving state-of-the-art results. We released our code at https: //github. com/bytedance/apm.

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ICML Conference 2025 Conference Paper

Demeaned Sparse: Efficient Anomaly Detection by Residual Estimate

Yifan Fang
Yifei Fang
Ruizhe Chen
Haote Xu
Xinghao Ding
Yue Huang 0001

Frequency-domain image anomaly detection methods can substantially enhance anomaly detection performance, however, they still lack an interpretable theoretical framework to guarantee the effectiveness of the detection process. We propose a novel test to detect anomalies in structural image via a Demeaned Fourier transform (DFT) under factor model framework, and we proof its effectiveness. We also briefly give the asymptotic theories of our test, the asymptotic theory explains why the test can detect anomalies at both the image and pixel levels within the theoretical lower bound. Based on our test, we derive a module called Demeaned Fourier Sparse (DFS) that effectively enhances detection performance in unsupervised anomaly detection tasks, which can construct masks in the Fourier domain and utilize a distribution-free sampling method similar to the bootstrap method. The experimental results indicate that this module can accurately and efficiently generate effective masks for reconstruction-based anomaly detection tasks, thereby enhancing the performance of anomaly detection methods and validating the effectiveness of the theoretical framework.

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ICLR Conference 2025 Conference Paper

FairMT-Bench: Benchmarking Fairness for Multi-turn Dialogue in Conversational LLMs

Zhiting Fan
Ruizhe Chen
Tianxiang Hu
Zuozhu Liu

The increasing deployment of large language model (LLM)-based chatbots has raised concerns regarding fairness. Fairness issues in LLMs may result in serious consequences, such as bias amplification, discrimination, and harm to minority groups. Many efforts are dedicated to evaluating and mitigating biases in LLMs. However, existing fairness benchmarks mainly focus on single-turn dialogues, while multi-turn scenarios, which better reflect real-world conversations, pose greater challenges due to conversational complexity and risk for bias accumulation. In this paper, we introduce a comprehensive benchmark for fairness of LLMs in multi-turn scenarios, **FairMT-Bench**. Specifically, We propose a task taxonomy to evaluate fairness of LLMs cross three stages: context understanding, interaction fairness, and fairness trade-offs, each comprising two tasks. To ensure coverage of diverse bias types and attributes, our multi-turn dialogue dataset FairMT-10K is constructed by integrating data from established fairness benchmarks. For evaluation, we employ GPT-4 along with bias classifiers like Llama-Guard-3, and human annotators to ensure robustness. Our experiments and analysis on FairMT-10K reveal that in multi-turn dialogue scenarios, LLMs are more prone to generating biased responses, showing significant variation in performance across different tasks and models. Based on these findings, we develop a more challenging dataset, FairMT-1K, and test 15 current state-of-the-art (SOTA) LLMs on this dataset. The results highlight the current state of fairness in LLMs and demonstrate the value of this benchmark for evaluating fairness of LLMs in more realistic multi-turn dialogue contexts. This underscores the need for future works to enhance LLM fairness and incorporate FairMT-1K in such efforts. Our code and dataset are available at https://github.com/FanZT6/FairMT-bench.

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NeurIPS Conference 2025 Conference Paper

FRN: Fractal-Based Recursive Spectral Reconstruction Network

Ge Meng
Zhongnan Cai
Ruizhe Chen
Jingyan Tu
Yingying Wang
Yue Huang
Xinghao Ding

Generating hyperspectral images (HSIs) from RGB images through spectral reconstruction can significantly reduce the cost of HSI acquisition. In this paper, we propose a Fractal-Based Recursive Spectral Reconstruction Network (FRN), which differs from existing paradigms that attempt to directly integrate the full-spectrum information from the R, G, and B channels in a one-shot manner. Instead, it treats spectral reconstruction as a progressive process, predicting from broad to narrow bands or employing a coarse-to-fine approach for predicting the next wavelength. Inspired by fractals in mathematics, FRN establishes a novel spectral reconstruction paradigm by recursively invoking an atomic reconstruction module. In each invocation, only the spectral information from neighboring bands is used to provide clues for the generation of the image at the next wavelength, which follows the low-rank property of spectral data. Moreover, we design a band-aware state space model that employs a pixel-differentiated scanning strategy at different stages of the generation process, further suppressing interference from low-correlation regions caused by reflectance differences. Through extensive experimentation across different datasets, FRN achieves superior reconstruction performance compared to state-of-the-art methods. Code is available at https: //github. com/mongko007/frn.

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IJCAI Conference 2025 Conference Paper

Modality-Fair Preference Optimization for Trustworthy MLLM Alignment

Songtao Jiang
Yan Zhang
Ruizhe Chen
Tianxiang Hu
Yeying Jin
Qinglin He
Yang Feng
Jian Wu

Multimodal large language models (MLLMs) have achieved remarkable success across various tasks. However, separate training of visual and textual encoders often results in a misalignment of the modality. Such misalignment may lead models to generate content that is absent from the input image, a phenomenon referred to as hallucination. These inaccuracies severely undermine the trustworthiness of MLLMs in real-world applications. Despite attempts to optimize text preferences to mitigate this issue, our initial investigation indicates that the trustworthiness of MLLMs remains inadequate. Specifically, these models tend to provide preferred answers even when the input image is heavily distorted. Analysis of visual token attention also indicates that the model focuses primarily on the surrounding context rather than the key object referenced in the question. These findings highlight a misalignment between the modalities, where answers inadequately leverage input images. Motivated by our findings, we propose Modality-Fair Preference Optimization (MFPO), which comprises three components: the construction of a multimodal preference dataset in which dispreferred images differ from originals solely in key regions; an image reward loss function encouraging the model to generate answers better aligned with the input images; and an easy-to-hard iterative alignment strategy to stabilize joint modality training. Extensive experiments on three trustworthiness benchmarks demonstrate that MFPO significantly enhances the trustworthiness of MLLMs. In particular, it enables the 7B models to attain trustworthiness levels on par with, or even surpass, those of the 13B, 34B, and larger models.

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ICLR Conference 2025 Conference Paper

PAD: Personalized Alignment of LLMs at Decoding-time

Ruizhe Chen
Xiaotian Zhang
Meng Luo
Wenhao Chai
Zuozhu Liu

Aligning with personalized preferences, which vary significantly across cultural, educational, and political differences, poses a significant challenge due to the computational costs and data demands of traditional alignment methods. In response, this paper presents Personalized Alignment at Decoding-time (PAD), a novel framework designed to align LLM outputs with diverse personalized preferences during the inference phase, eliminating the need for additional training. By introducing a unique personalized reward modeling strategy, this framework decouples the text generation process from personalized preferences, facilitating the generation of generalizable token-level personalized rewards. The PAD algorithm leverages these rewards to guide the decoding process, dynamically tailoring the base model’s predictions to personalized preferences. Extensive experimental results demonstrate that PAD not only outperforms existing training-based alignment methods in terms of aligning with diverse preferences but also shows significant generalizability to preferences unseen during training and scalability across different base models. This work advances the capability of LLMs to meet user needs in real-time applications, presenting a substantial step forward in personalized LLM alignment.

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NeurIPS Conference 2024 Conference Paper

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization

Xiangxin Zhou
Dongyu Xue
Ruizhe Chen
Zaixiang Zheng
Liang Wang
Quanquan Gu

Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nature. In this paper, we tackle antigen-specific antibody sequence-structure co-design as an optimization problem towards specific preferences, considering both rationality and functionality. Leveraging a pre-trained conditional diffusion model that jointly models sequences and structures of antibodies with equivariant neural networks, we propose direct energy-based preference optimization to guide the generation of antibodies with both rational structures and considerable binding affinities to given antigens. Our method involves fine-tuning the pre-trained diffusion model using a residue-level decomposed energy preference. Additionally, we employ gradient surgery to address conflicts between various types of energy, such as attraction and repulsion. Experiments on RAbD benchmark show that our approach effectively optimizes the energy of generated antibodies and achieves state-of-the-art performance in designing high-quality antibodies with low total energy and high binding affinity simultaneously, demonstrating the superiority of our approach.

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AAAI Conference 2024 Conference Paper

Robustness-Guided Image Synthesis for Data-Free Quantization

Jianhong Bai
Yuchen Yang
Huanpeng Chu
Hualiang Wang
Zuozhu Liu
Ruizhe Chen
Xiaoxuan He
Lianrui Mu

Quantization has emerged as a promising direction for model compression. Recently, data-free quantization has been widely studied as a promising method to avoid privacy concerns, which synthesizes images as an alternative to real training data. Existing methods use classification loss to ensure the reliability of the synthesized images. Unfortunately, even if these images are well-classified by the pre-trained model, they still suffer from low semantics and homogenization issues. Intuitively, these low-semantic images are sensitive to perturbations, and the pre-trained model tends to have inconsistent output when the generator synthesizes an image with low semantics. To this end, we propose Robustness-Guided Image Synthesis (RIS), a simple but effective method to enrich the semantics of synthetic images and improve image diversity, further boosting the performance of data-free compression tasks. Concretely, we first introduce perturbations on input and model weight, then define the inconsistency metrics at feature and prediction levels before and after perturbations. On the basis of inconsistency on two levels, we design a robustness optimization objective to eliminate low-semantic images. Moreover, we also make our approach diversity-aware by forcing the generator to synthesize images with small correlations. With RIS, we achieve state-of-the-art performance for various settings on data-free quantization and can be extended to other data-free compression tasks.

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NeurIPS Conference 2023 Conference Paper

Fast Model DeBias with Machine Unlearning

Ruizhe Chen
Jianfei Yang
Huimin Xiong
Jianhong Bai
Tianxiang Hu
Jin Hao
Yang Feng
Joey Tianyi Zhou

Recent discoveries have revealed that deep neural networks might behave in a biased manner in many real-world scenarios. For instance, deep networks trained on a large-scale face recognition dataset CelebA tend to predict blonde hair for females and black hair for males. Such biases not only jeopardize the robustness of models but also perpetuate and amplify social biases, which is especially concerning for automated decision-making processes in healthcare, recruitment, etc. , as they could exacerbate unfair economic and social inequalities among different groups. Existing debiasing methods suffer from high costs in bias labeling or model re-training, while also exhibiting a deficiency in terms of elucidating the origins of biases within the model. To this respect, we propose a fast model debiasing method (FMD) which offers an efficient approach to identify, evaluate and remove biases inherent in trained models. The FMD identifies biased attributes through an explicit counterfactual concept and quantifies the influence of data samples with influence functions. Moreover, we design a machine unlearning-based strategy to efficiently and effectively remove the bias in a trained model with a small counterfactual dataset. Experiments on the Colored MNIST, CelebA, and Adult Income datasets demonstrate that our method achieves superior or competing classification accuracies compared with state-of-the-art retraining-based methods while attaining significantly fewer biases and requiring much less debiasing cost. Notably, our method requires only a small external dataset and updating a minimal amount of model parameters, without the requirement of access to training data that may be too large or unavailable in practice.

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NeurIPS Conference 2023 Conference Paper

Towards Distribution-Agnostic Generalized Category Discovery

Jianhong Bai
Zuozhu Liu
Hualiang Wang
Ruizhe Chen
Lianrui Mu
Xiaomeng Li
Joey Tianyi Zhou
Yang Feng

Data imbalance and open-ended distribution are two intrinsic characteristics of the real visual world. Though encouraging progress has been made in tackling each challenge separately, few works dedicated to combining them towards real-world scenarios. While several previous works have focused on classifying close-set samples and detecting open-set samples during testing, it's still essential to be able to classify unknown subjects as human beings. In this paper, we formally define a more realistic task as distribution-agnostic generalized category discovery (DA-GCD): generating fine-grained predictions for both close- and open-set classes in a long-tailed open-world setting. To tackle the challenging problem, we propose a Self- Ba lanced Co -Advice co n trastive framework (BaCon), which consists of a contrastive-learning branch and a pseudo-labeling branch, working collaboratively to provide interactive supervision to resolve the DA-GCD task. In particular, the contrastive-learning branch provides reliable distribution estimation to regularize the predictions of the pseudo-labeling branch, which in turn guides contrastive learning through self-balanced knowledge transfer and a proposed novel contrastive loss. We compare BaCon with state-of-the-art methods from two closely related fields: imbalanced semi-supervised learning and generalized category discovery. The effectiveness of BaCon is demonstrated with superior performance over all baselines and comprehensive analysis across various datasets. Our code is publicly available.

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