Xuefeng Liu

Xuefeng Liu, Fangfang Xia, Rick L. Stevens et al.

While training models and labeling data are resource-intensive, a wealth of pre-trained models and unlabeled data exists. To effectively utilize these resources, we present an approach to actively select pre-trained models while minimizing labeling costs. We frame this as an online contextual active model selection problem: At each round, the learner receives an unlabeled data point as a context. The objective is to adaptively select the best model to make a prediction while limiting label requests. To tackle this problem, we propose CAMS, a contextual active model selection algorithm that relies on two novel components: (1) a contextual model selection mechanism, which leverages context information to make informed decisions about which model is likely to perform best for a given context, and (2) an active query component, which strategically chooses when to request labels for data points, minimizing the overall labeling cost. We provide rigorous theoretical analysis for the regret and query complexity under both adversarial and stochastic settings. Furthermore, we demonstrate the effectiveness of our algorithm on a diverse collection of benchmark classification tasks. Notably, CAMS requires substantially less labeling effort (less than 10%) compared to existing methods on CIFAR10 and DRIFT benchmarks, while achieving similar or better accuracy. Our code is publicly available at: https://github.com/xuefeng-cs/Contextual-Active-Model-Selection.

Xuefeng Liu, Takuma Yoneda, Chaoqi Wang et al.

Reinforcement learning (RL) has made significant strides in various complex domains. However, identifying an effective policy via RL often necessitates extensive exploration. Imitation learning aims to mitigate this issue by using expert demonstrations to guide exploration. In real-world scenarios, one often has access to multiple suboptimal black-box experts, rather than a single optimal oracle. These experts do not universally outperform each other across all states, presenting a challenge in actively deciding which oracle to use and in which state. We introduce MAPS and MAPS-SE, a class of policy improvement algorithms that perform imitation learning from multiple suboptimal oracles. In particular, MAPS actively selects which of the oracles to imitate and improve their value function estimates, and MAPS-SE additionally leverages an active state exploration criterion to determine which states one should explore. We provide a comprehensive theoretical analysis and demonstrate that MAPS and MAPS-SE enjoy sample efficiency advantage over the state-of-the-art policy improvement algorithms. Empirical results show that MAPS-SE significantly accelerates policy optimization via state-wise imitation learning from multiple oracles across a broad spectrum of control tasks in the DeepMind Control Suite. Our code is publicly available at: https://github.com/ripl/maps.

Guogang Zhu, Xuefeng Liu, Jianwei Niu et al.

In personalized federated learning (PFL), it is widely recognized that achieving both high model generalization and effective personalization poses a significant challenge due to their conflicting nature. As a result, existing PFL methods can only manage a trade-off between these two objectives. This raises an interesting question: Is it feasible to develop a model capable of achieving both objectives simultaneously? Our paper presents an affirmative answer, and the key lies in the observation that deep models inherently exhibit hierarchical architectures, which produce representations with various levels of generalization and personalization at different stages. A straightforward approach stemming from this observation is to select multiple representations from these layers and combine them to concurrently achieve generalization and personalization. However, the number of candidate representations is commonly huge, which makes this method infeasible due to high computational costs.To address this problem, we propose DualFed, a new method that can directly yield dual representations correspond to generalization and personalization respectively, thereby simplifying the optimization task. Specifically, DualFed inserts a personalized projection network between the encoder and classifier. The pre-projection representations are able to capture generalized information shareable across clients, and the post-projection representations are effective to capture task-specific information on local clients. This design minimizes the mutual interference between generalization and personalization, thereby achieving a win-win situation. Extensive experiments show that DualFed can outperform other FL methods. Code is available at https://github.com/GuogangZhu/DualFed.

Xuefeng Liu, Shin'ichi Oishi

The finite element method(FEM) is applied to bound leading eigenvalues of Laplace operator over polygonal domain. Compared with classical numerical methods, most of which can only give concrete eigenvalue bounds over special domain of symmetry, our proposed algorithm can provide concrete eigenvalue bounds for domain of arbitrary shape, even in the case that eigenfunction has singularity. The problem of eigenvalue estimation is solved in two steps. First, we construct computable a priori error estimation for FEM solution of Poisson's problem even for non-convex domain with re-entrant corner. Second, a new computable lower and upper bounds is developed for eigenvalues. As the interval arithmetic is implemented in the FEM computation, the desired eigenvalue bounds can be expected to be mathematically correct. The Lehmann's theorem is also adopted to sharpen the eigenvalue bounds with high precision. At the end of this paper, we illustrate several computation examples, such as the case of L-shaped domain and crack domain, to demonstrate the efficiency and flexibility of proposed method.

Chun'guang You, Hehu Xie, Xuefeng Liu

To provide mathematically rigorous eigenvalue bounds for the Steklov eigenvalue problem, an enhanced version of the eigenvalue estimation algorithm developed by the third author is proposed, which removes the requirements of the positive definiteness of bilinear forms in the formulation of eigenvalue problems. In practical eigenvalue estimation, the Crouzeix--Raviart finite element method (FEM) along with quantitative error estimation is adopted. Numerical experiments for eigenvalue problems defined on a square domain and an L-shaped domain are provided to validate the precision of computed eigenvalue bounds.

Hao Su, Xuefeng Liu, Jianwei Niu et al.

We propose 3Deformer, a general-purpose framework for interactive 3D shape editing. Given a source 3D mesh with semantic materials, and a user-specified semantic image, 3Deformer can accurately edit the source mesh following the shape guidance of the semantic image, while preserving the source topology as rigid as possible. Recent studies of 3D shape editing mostly focus on learning neural networks to predict 3D shapes, which requires high-cost 3D training datasets and is limited to handling objects involved in the datasets. Unlike these studies, our 3Deformer is a non-training and common framework, which only requires supervision of readily-available semantic images, and is compatible with editing various objects unlimited by datasets. In 3Deformer, the source mesh is deformed utilizing the differentiable renderer technique, according to the correspondences between semantic images and mesh materials. However, guiding complex 3D shapes with a simple 2D image incurs extra challenges, that is, the deform accuracy, surface smoothness, geometric rigidity, and global synchronization of the edited mesh should be guaranteed. To address these challenges, we propose a hierarchical optimization architecture to balance the global and local shape features, and propose further various strategies and losses to improve properties of accuracy, smoothness, rigidity, and so on. Extensive experiments show that our 3Deformer is able to produce impressive results and reaches the state-of-the-art level.

Xuefeng Liu, Takuma Yoneda, Rick L. Stevens et al.

While reinforcement learning (RL) has shown promising performance, its sample complexity continues to be a substantial hurdle, restricting its broader application across a variety of domains. Imitation learning (IL) utilizes oracles to improve sample efficiency, yet it is often constrained by the quality of the oracles deployed. which actively interleaves between IL and RL based on an online estimate of their performance. RPI draws on the strengths of IL, using oracle queries to facilitate exploration, an aspect that is notably challenging in sparse-reward RL, particularly during the early stages of learning. As learning unfolds, RPI gradually transitions to RL, effectively treating the learned policy as an improved oracle. This algorithm is capable of learning from and improving upon a diverse set of black-box oracles. Integral to RPI are Robust Active Policy Selection (RAPS) and Robust Policy Gradient (RPG), both of which reason over whether to perform state-wise imitation from the oracles or learn from its own value function when the learner's performance surpasses that of the oracles in a specific state. Empirical evaluations and theoretical analysis validate that RPI excels in comparison to existing state-of-the-art methodologies, demonstrating superior performance across various benchmark domains.

Xuefeng Liu, Songhao Jiang, Siyu Chen et al.

Finetuning a Large Language Model (LLM) is crucial for generating results towards specific objectives. This research delves into the realm of drug optimization and introduce a novel reinforcement learning algorithm to finetune a drug optimization LLM-based generative model, enhancing the original drug across target objectives, while retains the beneficial chemical properties of the original drug. This work is comprised of two primary components: (1) DrugImprover: A framework tailored for improving robustness and efficiency in drug optimization. It includes a LLM designed for drug optimization and a novel Structured Policy Optimization (SPO) algorithm, which is theoretically grounded. This algorithm offers a unique perspective for fine-tuning the LLM-based generative model by aligning the improvement of the generated molecule with the input molecule under desired objectives. (2) A dataset of 1 million compounds, each with OEDOCK docking scores on 5 human proteins associated with cancer cells and 24 binding sites from SARS-CoV-2 virus. We conduct a comprehensive evaluation of SPO and demonstrate its effectiveness in improving the original drug across target properties. Our code and dataset will be publicly available at: https://github.com/xuefeng-cs/DrugImproverGPT.

Tingzhi Li, Xuefeng Liu

Graph Neural Networks (GNNs) are increasingly deployed in graph-related applications, making ownership verification critical to protect their intellectual property against model theft. Fingerprinting and black-box watermarking are two main methods. However, the former relies on determining model similarity, which is computationally expensive and prone to ownership collisions after model post-processing such as model pruning or fine-tuning. The latter embeds backdoors, exposing watermarked models to the risk of backdoor attacks. Moreover, both methods enable ownership verification but do not convey additional information. As a result, each distributed model requires a unique trigger graph, and all trigger graphs must be used to query the suspect model during verification. Multiple queries increase the financial cost and the risk of detection. To address these challenges, this paper proposes WGLE, a novel black-box watermarking paradigm for GNNs that enables embedding the multi-bit string as the ownership information without using backdoors. WGLE builds on a key insight we term Layer-wise Distance Difference on an Edge (LDDE), which quantifies the difference between the feature distance and the prediction distance of two connected nodes. By predefining positive or negative LDDE values for multiple selected edges, WGLE embeds the watermark encoding the intended information without introducing incorrect mappings that compromise the primary task. WGLE is evaluated on six public datasets and six mainstream GNN architectures along with state-of-the-art methods. The results show that WGLE achieves 100% ownership verification accuracy, an average fidelity degradation of 0.85%, comparable robustness against potential attacks, and low embedding overhead. The code is available in the repository.

Xinghao Wu, Xuefeng Liu, Jianwei Niu et al.

To address data heterogeneity, the key strategy of Personalized Federated Learning (PFL) is to decouple general knowledge (shared among clients) and client-specific knowledge, as the latter can have a negative impact on collaboration if not removed. Existing PFL methods primarily adopt a parameter partitioning approach, where the parameters of a model are designated as one of two types: parameters shared with other clients to extract general knowledge and parameters retained locally to learn client-specific knowledge. However, as these two types of parameters are put together like a jigsaw puzzle into a single model during the training process, each parameter may simultaneously absorb both general and client-specific knowledge, thus struggling to separate the two types of knowledge effectively. In this paper, we introduce FedDecomp, a simple but effective PFL paradigm that employs parameter additive decomposition to address this issue. Instead of assigning each parameter of a model as either a shared or personalized one, FedDecomp decomposes each parameter into the sum of two parameters: a shared one and a personalized one, thus achieving a more thorough decoupling of shared and personalized knowledge compared to the parameter partitioning method. In addition, as we find that retaining local knowledge of specific clients requires much lower model capacity compared with general knowledge across all clients, we let the matrix containing personalized parameters be low rank during the training process. Moreover, a new alternating training strategy is proposed to further improve the performance. Experimental results across multiple datasets and varying degrees of data heterogeneity demonstrate that FedDecomp outperforms state-of-the-art methods up to 4.9\%. The code is available at https://github.com/XinghaoWu/FedDecomp.

Xuefeng Liu, Chih-chan Tien, Peng Ding et al.

The objective of drug discovery is to identify chemical compounds that possess specific pharmaceutical properties toward a binding target. Existing large language models (LLMS) can achieve high token matching scores in terms of likelihood for molecule generation. However, relying solely on LLM decoding often results in the generation of molecules that are either invalid due to a single misused token, or suboptimal due to unbalanced exploration and exploitation as a consequence of the LLMs prior experience. Here we propose ERP, Entropy-Reinforced Planning for Transformer Decoding, which employs an entropy-reinforced planning algorithm to enhance the Transformer decoding process and strike a balance between exploitation and exploration. ERP aims to achieve improvements in multiple properties compared to direct sampling from the Transformer. We evaluated ERP on the SARS-CoV-2 virus (3CLPro) and human cancer cell target protein (RTCB) benchmarks and demonstrated that, in both benchmarks, ERP consistently outperforms the current state-of-the-art algorithm by 1-5 percent, and baselines by 5-10 percent, respectively. Moreover, such improvement is robust across Transformer models trained with different objectives. Finally, to further illustrate the capabilities of ERP, we tested our algorithm on three code generation benchmarks and outperformed the current state-of-the-art approach as well. Our code is publicly available at: https://github.com/xuefeng-cs/ERP.

Xuefeng Liu, Songhao Jiang, Bo Li et al.

Large Language Models (LLMs) employ three popular training approaches: Masked Language Models (MLM), Causal Language Models (CLM), and Sequence-to-Sequence Models (seq2seq). However, each approach has its strengths and limitations, and faces challenges in addressing specific tasks that require controllable and bidirectional generation, such as drug optimization. To address this challenge, inspired by the biological processes of growth and evolution, which involve the expansion, shrinking, and mutation of sequences, we introduce ControllableGPT. This initiative represents the first effort to combine the advantages of MLM, CLM, and seq2seq into a single unified, controllable GPT framework. It enables the precise management of specific locations and ranges within a sequence, allowing for expansion, reduction, or mutation over chosen or random lengths, while maintaining the integrity of any specified positions or subsequences. In this work, we designed ControllableGPT for drug optimization from the ground up, which included proposing the Causally Masked Seq2seq (CMS) objective, developing the training corpus, introducing a novel pre-training approach, and devising a unique generation process. We demonstrate the effectiveness and controllability of ControllableGPT by conducting experiments on drug optimization tasks for both viral and cancer benchmarks, surpassing competing baselines.

Xuefeng Liu, Songhao Jiang, Ian Foster et al.

Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates retaining the beneficial properties of the original drug while simultaneously enhancing desired attributes beyond its scope. In this work, we aim to tackle this challenge by introducing ScaffoldGPT, a novel Generative Pretrained Transformer (GPT) designed for drug optimization based on molecular scaffolds. Our work comprises three key components: (1) A three-stage drug optimization approach that integrates pretraining, finetuning, and decoding optimization. (2) A novel two-phase incremental pre-training strategy for scaffold-based drug optimization. (3) A token-level decoding optimization strategy, Top-N, that enabling controlled, reward-guided generation using the pretrained or finetuned GPT. We demonstrate via a comprehensive evaluation on COVID and cancer benchmarks that ScaffoldGPT outperforms the competing baselines in drug optimization benchmarks, while excelling in preserving original functional scaffold and enhancing desired properties.

Xuefeng Liu, Mingxuan Cao, Songhao Jiang et al.

The goal of protein design is to generate amino acid sequences that fold into functional structures with desired properties. Prior methods combining autoregressive language models with Monte Carlo Tree Search (MCTS) struggle with long-range dependencies and suffer from an impractically large search space. We propose MCTD-ME, Monte Carlo Tree Diffusion with Multiple Experts, which integrates masked diffusion models with tree search to enable multi-token planning and efficient exploration. Unlike autoregressive planners, MCTD-ME uses biophysical-fidelity-enhanced diffusion denoising as the rollout engine, jointly revising multiple positions and scaling to large sequence spaces. It further leverages experts of varying capacities to enrich exploration, guided by a pLDDT-based masking schedule that targets low-confidence regions while preserving reliable residues. We propose a novel multi-expert selection rule (PH-UCT-ME) extends predictive-entropy UCT to expert ensembles. On the inverse folding task (CAMEO and PDB benchmarks), MCTD-ME outperforms single-expert and unguided baselines in both sequence recovery (AAR) and structural similarity (scTM), with gains increasing for longer proteins and benefiting from multi-expert guidance. More generally, the framework is model-agnostic and applicable beyond inverse folding, including de novo protein engineering and multi-objective molecular generation.

Xuefeng Liu, Songhao Jiang, Qinan Huang et al.

Fragment-Based Drug Discovery (FBDD) is a popular approach in early drug development, but designing effective linkers to combine disconnected molecular fragments into chemically and pharmacologically viable candidates remains challenging. Further complexity arises when fragments contain structural redundancies, like duplicate rings, which cannot be addressed by simply adding or removing atoms or bonds. To address these challenges in a unified framework, we introduce FragmentGPT, which integrates two core components: (1) a novel chemically-aware, energy-based bond cleavage pre-training strategy that equips the GPT-based model with fragment growing, linking, and merging capabilities, and (2) a novel Reward Ranked Alignment with Expert Exploration (RAE) algorithm that combines expert imitation learning for diversity enhancement, data selection and augmentation for Pareto and composite score optimality, and Supervised Fine-Tuning (SFT) to align the learner policy with multi-objective goals. Conditioned on fragment pairs, FragmentGPT generates linkers that connect diverse molecular subunits while simultaneously optimizing for multiple pharmaceutical goals. It also learns to resolve structural redundancies-such as duplicated fragments-through intelligent merging, enabling the synthesis of optimized molecules. FragmentGPT facilitates controlled, goal-driven molecular assembly. Experiments and ablation studies on real-world cancer datasets demonstrate its ability to generate chemically valid, high-quality molecules tailored for downstream drug discovery tasks.

Hao Su, Jianwei Niu, Xuefeng Liu et al.

Quick Response (QR) code is one of the most worldwide used two-dimensional codes.~Traditional QR codes appear as random collections of black-and-white modules that lack visual semantics and aesthetic elements, which inspires the recent works to beautify the appearances of QR codes. However, these works adopt fixed generation algorithms and therefore can only generate QR codes with a pre-defined style. In this paper, combining the Neural Style Transfer technique, we propose a novel end-to-end method, named ArtCoder, to generate the stylized QR codes that are personalized, diverse, attractive, and scanning-robust.~To guarantee that the generated stylized QR codes are still scanning-robust, we propose a Sampling-Simulation layer, a module-based code loss, and a competition mechanism. The experimental results show that our stylized QR codes have high-quality in both the visual effect and the scanning-robustness, and they are able to support the real-world application.

Xiaozheng Xie, Jianwei Niu, Xuefeng Liu et al.

Although deep learning models like CNNs have achieved great success in medical image analysis, the small size of medical datasets remains a major bottleneck in this area. To address this problem, researchers have started looking for external information beyond current available medical datasets. Traditional approaches generally leverage the information from natural images via transfer learning. More recent works utilize the domain knowledge from medical doctors, to create networks that resemble how medical doctors are trained, mimic their diagnostic patterns, or focus on the features or areas they pay particular attention to. In this survey, we summarize the current progress on integrating medical domain knowledge into deep learning models for various tasks, such as disease diagnosis, lesion, organ and abnormality detection, lesion and organ segmentation. For each task, we systematically categorize different kinds of medical domain knowledge that have been utilized and their corresponding integrating methods. We also provide current challenges and directions for future research.