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Can Chen

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9 papers

2 author rows

TMLR Journal 2026 Journal Article

Offline Model-Based Optimization: Comprehensive Review

Minsu Kim
Jiayao Gu
Ye Yuan
Taeyoung Yun
Zixuan Liu
Yoshua Bengio
Can Chen

Offline black-box optimization is a fundamental challenge in science and engineering, where the goal is to optimize black-box functions using only offline datasets. This setting is particularly relevant when querying the objective function is prohibitively expensive or infeasible, with applications spanning protein engineering, material discovery, neural architecture search, and beyond. The main difficulty lies in accurately estimating the objective landscape beyond the available data, where extrapolations are fraught with significant epistemic uncertainty. This uncertainty can lead to objective hacking (reward hacking)—exploiting model inaccuracies in unseen regions—or other spurious optimizations that yield misleadingly high performance estimates outside the offline distribution. Recent advances in model-based optimization (MBO) have harnessed the generalization capabilities of deep neural networks to develop offline-specific surrogate and generative models. Trained with carefully designed strategies, these models are more robust against out-of-distribution issues, facilitating the discovery of improved designs. Despite its growing impact in accelerating scientific discovery, the field lacks a comprehensive review. To bridge this gap, we present the first thorough review of offline MBO. We begin by formalizing the problem for both single-objective and multi-objective settings and by reviewing recent benchmarks and evaluation metrics. We then categorize existing approaches into two key areas: surrogate modeling, which emphasizes accurate function approximation in out-of-distribution regions, and generative modeling, which explores high-dimensional design spaces to identify high-performing designs. Finally, we examine the key challenges and propose promising directions for advancement in this rapidly evolving field including safe control of superintelligent systems.

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ICML Conference 2025 Conference Paper

AffinityFlow: Guided Flows for Antibody Affinity Maturation

Can Chen
Karla-Luise Herpoldt
Chenchao Zhao
Zichen Wang
Marcus D. Collins
Shang Shang
Ron Benson

Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity. This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an alternating optimization framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a structure-based predictor, then (2) applies inverse folding to create sequence mutations, refined by a sequence-based predictor. A key challenge is the lack of labeled data for training both predictors. To address this, we develop a co-teaching module that incorporates valuable information from noisy biophysical energies into predictor refinement. The sequence-based predictor selects consensus samples to teach the structure-based predictor, and vice versa. Our method, AffinityFlow, achieves state-of-the-art performance in proof-of-concept affinity maturation experiments.

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TMLR Journal 2025 Journal Article

Design Editing for Offline Model-based Optimization

Ye Yuan
Youyuan Zhang
Can Chen
Haolun Wu
Melody Zixuan Li
Jianmo Li
James J. Clark
Xue Liu

Offline model-based optimization (MBO) aims to maximize a black-box objective function using only an offline dataset of designs and scores. These tasks span various domains, such as robotics, material design, and protein and molecular engineering. A common approach involves training a surrogate model using existing designs and their corresponding scores, and then generating new designs through gradient-based updates with respect to the surrogate model. This method suffers from the out-of-distribution issue, where the surrogate model may erroneously predict high scores for unseen designs. To address this challenge, we introduce a novel method, Design Editing for Offline Model-based Optimization} (DEMO), which leverages a diffusion prior to calibrate overly optimized designs. DEMO first generates pseudo design candidates by performing gradient ascent with respect to a surrogate model. While these pseudo design candidates contain information beyond the offline dataset, they might be invalid or have erroneously high predicted scores. Therefore, to address this challenge while utilizing the information provided by pseudo design candidates, we propose an editing process to refine these pseudo design candidates. We introduce noise to the pseudo design candidates and subsequently denoise them with a diffusion prior trained on the offline dataset, ensuring they align with the distribution of valid designs. Empirical evaluations on seven offline MBO tasks show that, with properly tuned hyperparamters, DEMO's score is competitive with the best previously reported scores in the literature.

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AAAI Conference 2025 Conference Paper

Fast and Interpretable Mixed-Integer Linear Program Solving by Learning Model Reduction

Yixuan Li
Can Chen
Jiajun Li
Jiahui Duan
Xiongwei Han
Tao Zhong
Vincent Chau
Weiwei Wu

By exploiting the correlation between the structure and the solution of Mixed-Integer Linear Programming (MILP), Machine Learning (ML) has become a promising method for solving large-scale MILP problems. Existing ML-based MILP solvers mainly focus on end-to-end solution learning, which suffers from the scalability issue due to the high dimensionality of the solution space. Instead of directly learning the optimal solution, this paper aims to learn a reduced and equivalent model of the original MILP as an intermediate step. The reduced model often corresponds to interpretable operations and is much simpler, enabling us to solve large-scale MILP problems much faster than existing commercial solvers. However, current approaches rely only on the optimal reduced model, overlooking the significant preference information of all reduced models. To address this issue, this paper proposes a preference-based model reduction learning method, which considers the relative performance (i.e., objective cost and constraint feasibility) of all reduced models on each MILP instance as preferences. We also introduce an attention mechanism to capture and represent preference information, which helps improve the performance of model reduction learning tasks. Moreover, we propose a SetCover based pruning method to control the number of reduced models (i.e., labels), thereby simplifying the learning process. Evaluation on real-world MILP problems shows that 1) compared to the state-of-the-art model reduction ML methods, our method obtains nearly 20% improvement on solution accuracy, and 2) compared to the commercial solver Gurobi, two to four orders of magnitude speedups are achieved.

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TMLR Journal 2025 Journal Article

LLM-TS Integrator: Integrating LLM for Enhanced Time Series Modeling

Can Chen
Gabriel L. Oliveira
Hossein Sharifi-Noghabi
Tristan Sylvain

Time series~(TS) modeling is essential in dynamic systems like weather prediction and anomaly detection. Recent studies utilize Large Language Models (LLMs) for TS modeling, leveraging their powerful pattern recognition capabilities. These methods primarily position LLMs as the predictive backbone, often omitting the mathematical modeling within traditional TS models, such as periodicity. However, disregarding the potential of LLMs also overlooks their pattern recognition capabilities. To address this gap, we introduce \textit{LLM-TS Integrator}, a novel framework that effectively integrates the capabilities of LLMs into traditional TS modeling. Central to this integration is our \textit{mutual information} module. The core of this \textit{mutual information} module is a traditional TS model enhanced with LLM-derived insights for improved predictive abilities. This enhancement is achieved by maximizing the mutual information between traditional model's TS representations and LLM's textual representation counterparts, bridging the two modalities. Moreover, we recognize that samples vary in importance for two losses: traditional prediction and mutual information maximization. To address this variability, we introduce the \textit{sample reweighting} module to improve information utilization. This module assigns dual weights to each sample: one for prediction loss and another for mutual information loss, dynamically optimizing these weights via bi-level optimization. Our method achieves state-of-the-art or comparable performance across five mainstream TS tasks, including short-term and long-term forecasting, imputation, classification, and anomaly detection. Our code is available at: \url{https://anonymous.4open.science/r/llm_ts_anonymous-F07D/README.MD}

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ICML Conference 2025 Conference Paper

Online Detection of LLM-Generated Texts via Sequential Hypothesis Testing by Betting

Can Chen
Jun-Kun Wang

Developing algorithms to differentiate between machine-generated texts and human-written texts has garnered substantial attention in recent years. Existing methods in this direction typically concern an offline setting where a dataset containing a mix of real and machine-generated texts is given upfront, and the task is to determine whether each sample in the dataset is from a large language model (LLM) or a human. However, in many practical scenarios, sources such as news websites, social media accounts, and online forums publish content in a streaming fashion. Therefore, in this online scenario, how to quickly and accurately determine whether the source is an LLM with strong statistical guarantees is crucial for these media or platforms to function effectively and prevent the spread of misinformation and other potential misuse of LLMs. To tackle the problem of online detection, we develop an algorithm based on the techniques of sequential hypothesis testing by betting that not only builds upon and complements existing offline detection techniques but also enjoys statistical guarantees, which include a controlled false positive rate and the expected time to correctly identify a source as an LLM. Experiments were conducted to demonstrate the effectiveness of our method.

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TMLR Journal 2024 Journal Article

Robust Guided Diffusion for Offline Black-Box Optimization

Can Chen
Christopher Beckham
Zixuan Liu
Xue Liu
Christopher Pal

Offline black-box optimization aims to maximize a black-box function using an offline dataset of designs and their measured properties. Two main approaches have emerged: the forward approach, which learns a mapping from input to its value, thereby acting as a proxy to guide optimization, and the inverse approach, which learns a mapping from value to input for conditional generation. (a) Although proxy-free~(classifier-free) diffusion shows promise in robustly modeling the inverse mapping, it lacks explicit guidance from proxies, essential for generating high-performance samples beyond the training distribution. Therefore, we propose \textit{proxy-enhanced sampling} which utilizes the explicit guidance from a trained proxy to bolster proxy-free diffusion with enhanced sampling control. (b) Yet, the trained proxy is susceptible to out-of-distribution issues. To address this, we devise the module \textit{diffusion-based proxy refinement}, which seamlessly integrates insights from proxy-free diffusion back into the proxy for refinement. To sum up, we propose \textit{\textbf{R}obust \textbf{G}uided \textbf{D}iffusion for Offline Black-box Optimization}~(\textbf{RGD}), combining the advantages of proxy~(explicit guidance) and proxy-free diffusion~(robustness) for effective conditional generation. RGD achieves state-of-the-art results on various design-bench tasks, underscoring its efficacy. Our code is \href{https://github.com/GGchen1997/RGD}{here}.

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NeurIPS Conference 2022 Conference Paper

Bidirectional Learning for Offline Infinite-width Model-based Optimization

Can Chen
Yingxueff Zhang
Jie Fu
Xue (Steve) Liu
Mark Coates

In offline model-based optimization, we strive to maximize a black-box objective function by only leveraging a static dataset of designs and their scores. This problem setting arises in numerous fields including the design of materials, robots, DNAs, proteins, etc. Recent approaches train a deep neural network (DNN) model on the static dataset to act as a proxy function, and then perform gradient ascent on the existing designs to obtain potentially high-scoring designs. This methodology frequently suffers from the out-of-distribution problem where the proxy function often returns adversarial designs. To mitigate this problem, we propose $\textit{\textbf{B}i\textbf{D}irectional learning for offline \textbf{I}nfinite-width model-based optimization}~(\textbf{BDI})$. BDI consists of two mappings: the forward mapping leverages the static dataset to predict the scores of the high-scoring designs, and the backward mapping leverages the high-scoring designs to predict the scores of the static dataset. The backward mapping, neglected in previous work, can distill more information of the static dataset into the high-scoring designs, which effectively mitigates the out-of-distribution problem. Yet, for a finite-width DNN model, the loss function of the backward mapping is intractable and only has an approximate form, which leads to a significant deterioration of the design quality. We thus adopt an infinite-width DNN model and propose to employ the corresponding neural tangent kernel to yield a closed-form loss for more accurate design updates. Experiments on various tasks verify the effectiveness of BDI. The code is available [here](https: //github. com/GGchen1997/BDI).

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NeurIPS Conference 2021 Conference Paper

Generalized DataWeighting via Class-Level Gradient Manipulation

Can Chen
Shuhao Zheng
Xi Chen
Erqun Dong
Xue (Steve) Liu
Hao Liu
Dejing Dou

Label noise and class imbalance are two major issues coexisting in real-world datasets. To alleviate the two issues, state-of-the-art methods reweight each instance by leveraging a small amount of clean and unbiased data. Yet, these methods overlook class-level information within each instance, which can be further utilized to improve performance. To this end, in this paper, we propose Generalized Data Weighting (GDW) to simultaneously mitigate label noise and class imbalance by manipulating gradients at the class level. To be specific, GDW unrolls the loss gradient to class-level gradients by the chain rule and reweights the flow of each gradient separately. In this way, GDW achieves remarkable performance improvement on both issues. Aside from the performance gain, GDW efficiently obtains class-level weights without introducing any extra computational cost compared with instance weighting methods. Specifically, GDW performs a gradient descent step on class-level weights, which only relies on intermediate gradients. Extensive experiments in various settings verify the effectiveness of GDW. For example, GDW outperforms state-of-the-art methods by $2. 56\%$ under the $60\%$ uniform noise setting in CIFAR10. Our code is available at https: //github. com/GGchen1997/GDW-NIPS2021.

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