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.

Xinghao Wu, Xuefeng Liu, Jianwei Niu et al.

Personalized federated learning (PFL) reduces the impact of non-independent and identically distributed (non-IID) data among clients by allowing each client to train a personalized model when collaborating with others. A key question in PFL is to decide which parameters of a client should be localized or shared with others. In current mainstream approaches, all layers that are sensitive to non-IID data (such as classifier layers) are generally personalized. The reasoning behind this approach is understandable, as localizing parameters that are easily influenced by non-IID data can prevent the potential negative effect of collaboration. However, we believe that this approach is too conservative for collaboration. For example, for a certain client, even if its parameters are easily influenced by non-IID data, it can still benefit by sharing these parameters with clients having similar data distribution. This observation emphasizes the importance of considering not only the sensitivity to non-IID data but also the similarity of data distribution when determining which parameters should be localized in PFL. This paper introduces a novel guideline for client collaboration in PFL. Unlike existing approaches that prohibit all collaboration of sensitive parameters, our guideline allows clients to share more parameters with others, leading to improved model performance. Additionally, we propose a new PFL method named FedCAC, which employs a quantitative metric to evaluate each parameter's sensitivity to non-IID data and carefully selects collaborators based on this evaluation. Experimental results demonstrate that FedCAC enables clients to share more parameters with others, resulting in superior performance compared to state-of-the-art methods, particularly in scenarios where clients have diverse distributions.

Xuefeng Liu, Fumio Kikuchi

The non-conforming linear ($P_1$) triangular FEM can be viewed as a kind of the discontinuous Galerkin method, and is attractive in both theoretical and practical senses. Since various error constants must be quantitatively evaluated for its accurate a priori and a posteriori error estimates, we derive their theoretical upper bounds and some computational results. In particular, the Babu$\check{s}$ka-Aziz maximum angle condition is required just as in the case of the conforming $P_1$ triangle. Some applications and numerical results are also illustrated to see the validity and effectiveness of our analysis.

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.

Qin Li, Xuefeng Liu

The paper develops an explicit a priori error estimate for finite element solution to nonhomogeneous Neumann problems. For this purpose, the hypercircle equation over finite element spaces is constructed and the explicit upper bound of the constant in the trace theorem is given. Numerical examples are shown in the final section, which implies the proposed error {estimate} has the convergence rate as $0.5$.

Xuefeng Liu, Chun'guang You

For the quadratic Lagrange interpolation function, an algorithm is proposed to provide explicit and verified bound for the interpolation error constant that appears in the interpolation error estimation. The upper bound for the interpolation constant is obtained by solving an eigenvalue problem along with explicit lower bound for its eigenvalues. The lower bound for interpolation constant can be easily obtained by applying the Rayleigh-Ritz method. Numerical computation is performed to demonstrate the sharpness of lower and upper bounds of the interpolation constants over triangles of different shapes. An online computing demo is available at http://www.xfliu.org/onlinelab/.

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.

Haolin Wang, Xuefeng Liu, Jianwei Niu et al.

Federated learning (FL) is a new paradigm for distributed machine learning that allows a global model to be trained across multiple clients without compromising their privacy. Although FL has demonstrated remarkable success in various scenarios, recent studies mainly utilize shallow and small neural networks. In our research, we discover a significant performance decline when applying the existing FL framework to deeper neural networks, even when client data are independently and identically distributed (i.i.d.). Our further investigation shows that the decline is due to the continuous accumulation of dissimilarities among client models during the layer-by-layer back-propagation process, which we refer to as "divergence accumulation." As deeper models involve a longer chain of divergence accumulation, they tend to manifest greater divergence, subsequently leading to performance decline. Both theoretical derivations and empirical evidence are proposed to support the existence of divergence accumulation and its amplified effects in deeper models. To address this issue, we propose several technical guidelines based on reducing divergence, such as using wider models and reducing the receptive field. These approaches can greatly improve the accuracy of FL on deeper models. For example, the application of these guidelines can boost the ResNet101 model's performance by as much as 43\% on the Tiny-ImageNet dataset.

Xinghao Wu, Xuefeng Liu, Jianwei Niu et al.

Personalized Federated Learning (PFL) is a commonly used framework that allows clients to collaboratively train their personalized models. PFL is particularly useful for handling situations where data from different clients are not independent and identically distributed (non-IID). Previous research in PFL implicitly assumes that clients can gain more benefits from those with similar data distributions. Correspondingly, methods such as personalized weight aggregation are developed to assign higher weights to similar clients during training. We pose a question: can a client benefit from other clients with dissimilar data distributions and if so, how? This question is particularly relevant in scenarios with a high degree of non-IID, where clients have widely different data distributions, and learning from only similar clients will lose knowledge from many other clients. We note that when dealing with clients with similar data distributions, methods such as personalized weight aggregation tend to enforce their models to be close in the parameter space. It is reasonable to conjecture that a client can benefit from dissimilar clients if we allow their models to depart from each other. Based on this idea, we propose DiversiFed which allows each client to learn from clients with diversified data distribution in personalized federated learning. DiversiFed pushes personalized models of clients with dissimilar data distributions apart in the parameter space while pulling together those with similar distributions. In addition, to achieve the above effect without using prior knowledge of data distribution, we design a loss function that leverages the model similarity to determine the degree of attraction and repulsion between any two models. Experiments on several datasets show that DiversiFed can benefit from dissimilar clients and thus outperform the state-of-the-art methods.

Xinghao Wu, Jianwei Niu, Xuefeng Liu et al.

In traditional Federated Learning approaches like FedAvg, the global model underperforms when faced with data heterogeneity. Personalized Federated Learning (PFL) enables clients to train personalized models to fit their local data distribution better. However, we surprisingly find that the feature extractor in FedAvg is superior to those in most PFL methods. More interestingly, by applying a linear transformation on local features extracted by the feature extractor to align with the classifier, FedAvg can surpass the majority of PFL methods. This suggests that the primary cause of FedAvg's inadequate performance stems from the mismatch between the locally extracted features and the classifier. While current PFL methods mitigate this issue to some extent, their designs compromise the quality of the feature extractor, thus limiting the full potential of PFL. In this paper, we propose a new PFL framework called FedPFT to address the mismatch problem while enhancing the quality of the feature extractor. FedPFT integrates a feature transformation module, driven by personalized prompts, between the global feature extractor and classifier. In each round, clients first train prompts to transform local features to match the global classifier, followed by training model parameters. This approach can also align the training objectives of clients, reducing the impact of data heterogeneity on model collaboration. Moreover, FedPFT's feature transformation module is highly scalable, allowing for the use of different prompts to tailor local features to various tasks. Leveraging this, we introduce a collaborative contrastive learning task to further refine feature extractor quality. Our experiments demonstrate that FedPFT outperforms state-of-the-art methods by up to 7.08%.

Guogang Zhu, Xuefeng Liu, Shaojie Tang et al.

Personalized federated learning (PFL) is a popular framework that allows clients to have different models to address application scenarios where clients' data are in different domains. The typical model of a client in PFL features a global encoder trained by all clients to extract universal features from the raw data and personalized layers (e.g., a classifier) trained using the client's local data. Nonetheless, due to the differences between the data distributions of different clients (aka, domain gaps), the universal features produced by the global encoder largely encompass numerous components irrelevant to a certain client's local task. Some recent PFL methods address the above problem by personalizing specific parameters within the encoder. However, these methods encounter substantial challenges attributed to the high dimensionality and non-linearity of neural network parameter space. In contrast, the feature space exhibits a lower dimensionality, providing greater intuitiveness and interpretability as compared to the parameter space. To this end, we propose a novel PFL framework named FedPick. FedPick achieves PFL in the low-dimensional feature space by selecting task-relevant features adaptively for each client from the features generated by the global encoder based on its local data distribution. It presents a more accessible and interpretable implementation of PFL compared to those methods working in the parameter space. Extensive experimental results show that FedPick could effectively select task-relevant features for each client and improve model performance in cross-domain FL.

Kingsley Yeon, Xuefeng Liu, Promit Ghosal

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

Rui Zhang, Jianwei Niu, Xuefeng Liu et al.

The Job-Shop Scheduling Problem (JSSP), under various forms of manufacturing uncertainty, has recently attracted considerable research attention. Most existing studies focus on parameter uncertainty, such as variable processing times, and typically adopt the actor-critic framework. In this paper, we explore a different but prevalent form of uncertainty in JSSP: structural uncertainty. Structural uncertainty arises when a job may follow one of several routing paths, and the selection is determined not by policy, but by situational factors (e.g., the quality of intermediate products) that cannot be known in advance. Existing methods struggle to address this challenge due to incorrect credit assignment: a high-quality action may be unfairly penalized if it is followed by a time-consuming path. To address this problem, we propose a novel method named UP-AAC. In contrast to conventional actor-critic methods, UP-AAC employs an asymmetric architecture. While its actor receives a standard stochastic state, the critic is crucially provided with a deterministic state reconstructed in hindsight. This design allows the critic to learn a more accurate value function, which in turn provides a lower-variance policy gradient to the actor, leading to more stable learning. In addition, we design an attention-based Uncertainty Perception Model (UPM) to enhance the actor's scheduling decisions. Extensive experiments demonstrate that our method outperforms existing approaches in reducing makespan on benchmark instances.

Xuefeng Liu, Songhao Jiang, Xiaotian Duan et al.

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges in life sciences, including therapeutic design, protein engineering, enzyme optimization, and elucidating biological mechanisms. Much work has been devoted to predicting binding affinity over the past decades. Here, we review recent significant works, with a focus on methods, evaluation strategies, and benchmark datasets. We note growing use of both traditional machine learning and deep learning models for predicting binding affinity, accompanied by an increasing amount of data on proteins and small drug-like molecules. With improved predictive performance and the FDA's phasing out of animal testing, AI-driven in silico models, such as AI virtual cells (AIVCs), are poised to advance binding affinity prediction; reciprocally, progress in building binding affinity predictors can refine AIVCs. Future efforts in binding affinity prediction and AI-driven in silico models can enhance the simulation of temporal dynamics, cell-type specificity, and multi-omics integration to support more accurate and personalized outcomes.

Taiga Nakano, Xuefeng Liu

For the finite element solution of Poisson's equation, a local a posteriori error estimation based on the Hypercircle method is proposed. Even for the solution of Poisson's equation without the $H^2$ regularity, this method can provide explicit local error estimation. The efficiency of the proposed method is demonstrated by numerical experiments for the boundary value problem of Poisson's equation defined on the 2D and 3D 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.

Zakaria Shams Siam, Xuefeng Liu, Chong Liu

In this paper, we formulate the new multi-objective coverage (MOC) problem where our goal is to identify a small set of representative samples whose predicted outcomes broadly cover the feasible multi-objective space. This problem is of great importance in many critical real-world applications, e.g., drug discovery and materials design, as this representative set can be evaluated much faster than the whole feasible set, thus significantly accelerating the scientific discovery process. Existing works cannot be directly applied as they either focus on sample space coverage or multi-objective optimization that targets the Pareto front. However, chemically diverse samples often yield identical objective profiles, and safety constraints are usually defined on the objectives. To solve this MOC problem, we propose a novel search algorithm, MOC-CAS, which employs an upper confidence bound-based acquisition function to select optimistic samples guided by Gaussian process posterior predictions. For enabling efficient optimization, we develop a smoothed relaxation of the hard feasibility test and derive an approximate optimizer. Compared to the competitive baselines, we show that our MOC-CAS empirically achieves superior performances across large-scale protein-target datasets for SARS-CoV-2 and cancer, each assessed on five objectives derived from SMILES-based features.

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.

Hao Su, Jianwei Niu, Xuefeng Liu et al.

Manga is a fashionable Japanese-style comic form that is composed of black-and-white strokes and is generally displayed as raster images on digital devices. Typical mangas have simple textures, wide lines, and few color gradients, which are vectorizable natures to enjoy the merits of vector graphics, e.g., adaptive resolutions and small file sizes. In this paper, we propose MARVEL (MAnga's Raster to VEctor Learning), a primitive-wise approach for vectorizing raster mangas by Deep Reinforcement Learning (DRL). Unlike previous learning-based methods which predict vector parameters for an entire image, MARVEL introduces a new perspective that regards an entire manga as a collection of basic primitives\textemdash stroke lines, and designs a DRL model to decompose the target image into a primitive sequence for achieving accurate vectorization. To improve vectorization accuracies and decrease file sizes, we further propose a stroke accuracy reward to predict accurate stroke lines, and a pruning mechanism to avoid generating erroneous and repeated strokes. Extensive subjective and objective experiments show that our MARVEL can generate impressive results and reaches the state-of-the-art level. Our code is open-source at: https://github.com/SwordHolderSH/Mang2Vec.

Zhengsu Chen, Lingxi Xie, Jianwei Niu et al.

The past year has witnessed the rapid development of applying the Transformer module to vision problems. While some researchers have demonstrated that Transformer-based models enjoy a favorable ability of fitting data, there are still growing number of evidences showing that these models suffer over-fitting especially when the training data is limited. This paper offers an empirical study by performing step-by-step operations to gradually transit a Transformer-based model to a convolution-based model. The results we obtain during the transition process deliver useful messages for improving visual recognition. Based on these observations, we propose a new architecture named Visformer, which is abbreviated from the `Vision-friendly Transformer'. With the same computational complexity, Visformer outperforms both the Transformer-based and convolution-based models in terms of ImageNet classification accuracy, and the advantage becomes more significant when the model complexity is lower or the training set is smaller. The code is available at https://github.com/danczs/Visformer.

Zhengsu Chen, Jianwei Niu, Lingxi Xie et al.

Automatic designing computationally efficient neural networks has received much attention in recent years. Existing approaches either utilize network pruning or leverage the network architecture search methods. This paper presents a new framework named network adjustment, which considers network accuracy as a function of FLOPs, so that under each network configuration, one can estimate the FLOPs utilization ratio (FUR) for each layer and use it to determine whether to increase or decrease the number of channels on the layer. Note that FUR, like the gradient of a non-linear function, is accurate only in a small neighborhood of the current network. Hence, we design an iterative mechanism so that the initial network undergoes a number of steps, each of which has a small `adjusting rate' to control the changes to the network. The computational overhead of the entire search process is reasonable, i.e., comparable to that of re-training the final model from scratch. Experiments on standard image classification datasets and a wide range of base networks demonstrate the effectiveness of our approach, which consistently outperforms the pruning counterpart. The code is available at https://github.com/danczs/NetworkAdjustment.

Xinghao Wu, Jianwei Niu, Guogang Zhu et al.

Heterogeneous federated learning (HtFL) aims to enable collaboration among clients that differ in both data distributions and model architectures. Prototype-based methods, which communicate class-level feature centers (prototypes) instead of full model parameters, have recently shown strong potential for HtFL. Existing prototype-based HtFL methods typically reuse the MSE-based or cosine-based alignment mechanism developed for homogeneous FL when aligning client-specific representations with global prototypes. These approaches are essentially coordinate alignment, where representations of clients are forced to match the global prototypes in the embedding space in an element-wise manner. Such alignment implicitly assumes that all clients should map their representations into the feature subspace defined by the global prototypes. This assumption is reasonable in homogeneous FL, where all clients share the same feature extractor. However, it becomes problematic in HtFL, since heterogeneous feature extractors naturally induce client-specific feature subspaces, and forcing all clients to optimize within a single global subspace unnecessarily suppresses their learning capacity. We observe that coordinate alignment implicitly couples two distinct objectives: aligning inter-class semantic structure, which is directly beneficial for classification, and enforcing a shared feature basis, which is unnecessary and even harmful under model heterogeneity. Building on this insight, we design FedSAF, which shifts the alignment objective from absolute coordinates to inter-class relational structure. We demonstrate that structural alignment consistently outperforms coordinate alignment in heterogeneous settings. Experiments on multiple benchmarks show that our structural alignment outperforms state-of-the-art prototype-based HtFL methods by up to 3.52\%.

Xuefeng Liu

We present, to the best of our knowledge, the first numerical algorithm for explicit, computable two-sided eigenvalue bounds for Schrödinger operators H = -Delta + V on R^N, N = 2,3, in the presence of both an unbounded potential and an unbounded domain. "Explicit" here means that all constants and ingredients are derived in closed form from the mesh, the potential, and a small set of explicit inequalities (Payne-Weinberger, Hardy, and explicit bounded-domain Sobolev embeddings); the conversion to fully verified(IEEE-754-safe, interval-arithmetic) enclosures is a separate verification step and is left for future work. In particular, singular attractive potentials of Coulomb type, V(x) = -Z/|x|, which model the hydrogen atom and the H_2^+ molecular ion, are covered by the theory. The method combines domain truncation to a bounded domain D(R) containing {|x| <= R} with an extension of Liu's Composite Enriched Crouzeix-Raviart (CECR) finite element method to sign-indefinite potentials. Upper bounds come from the standard conforming Galerkin method; lower bounds come from the CECR construction, whose gap to the exact eigenvalue closes as the mesh is refined. Numerical experiments on the 2D single- and two-centred Coulomb potentials and on the 3D hydrogen atom and H_2^+ molecular ion illustrate the algorithm and confirm the predicted convergence.

Yoel Zimmermann, Adib Bazgir, Zartashia Afzal et al.

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

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, Hung T. C. Le, Siyu Chen et al.

Online reinforcement learning (RL) enhances policies through direct interactions with the environment, but faces challenges related to sample efficiency. In contrast, offline RL leverages extensive pre-collected data to learn policies, but often produces suboptimal results due to limited data coverage. Recent efforts integrate offline and online RL in order to harness the advantages of both approaches. However, effectively combining online and offline RL remains challenging due to issues that include catastrophic forgetting, lack of robustness to data quality and limited sample efficiency in data utilization. In an effort to address these challenges, we introduce A3RL, which incorporates a novel confidence aware Active Advantage Aligned (A3) sampling strategy that dynamically prioritizes data aligned with the policy's evolving needs from both online and offline sources, optimizing policy improvement. Moreover, we provide theoretical insights into the effectiveness of our active sampling strategy and conduct diverse empirical experiments and ablation studies, demonstrating that our method outperforms competing online RL techniques that leverage offline data.

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, Songhao Jiang, Chih-chan Tien et al.

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural context. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. This bidirectional and hierarchical (Bi-Hierarchical) fusion approach leverages the strengths of both modalities to capture richer and more comprehensive protein representations. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including enzyme EC classification, model quality assessment, protein-ligand binding affinity prediction, protein-protein binding site prediction, and B cell epitopes prediction. Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of Bi-Hierarchical Fusion in bridging sequence and structural modalities.

Haolin Wang, Xuefeng Liu, Jianwei Niu et al.

Federated learning is a distributed machine learning paradigm designed to protect user data privacy, which has been successfully implemented across various scenarios. In traditional federated learning, the entire parameter set of local models is updated and averaged in each training round. Although this full network update method maximizes knowledge acquisition and sharing for each model layer, it prevents the layers of the global model from cooperating effectively to complete the tasks of each client, a challenge we refer to as layer mismatch. This mismatch problem recurs after every parameter averaging, consequently slowing down model convergence and degrading overall performance. To address the layer mismatch issue, we introduce the FedPart method, which restricts model updates to either a single layer or a few layers during each communication round. Furthermore, to maintain the efficiency of knowledge acquisition and sharing, we develop several strategies to select trainable layers in each round, including sequential updating and multi-round cycle training. Through both theoretical analysis and experiments, our findings demonstrate that the FedPart method significantly surpasses conventional full network update strategies in terms of convergence speed and accuracy, while also reducing communication and computational overheads.

Yuwei Cheng, Fan Yao, Xuefeng Liu et al.

This paper studies Learning from Imperfect Human Feedback (LIHF), addressing the potential irrationality or imperfect perception when learning from comparative human feedback. Building on evidences that human's imperfection decays over time (i.e., humans learn to improve), we cast this problem as a concave-utility continuous-action dueling bandit but under a restricted form of corruption: i.e., the corruption scale is decaying over time as $t^{ρ-1}$ for some "imperfection rate" $ρ\in [0, 1]$. With $T$ as the total number of iterations, we establish a regret lower bound of $ Ω(\max\{\sqrt{T}, T^ρ\}) $ for LIHF, even when $ρ$ is known. For the same setting, we develop the Robustified Stochastic Mirror Descent for Imperfect Dueling (RoSMID) algorithm, which achieves nearly optimal regret $\tilde{\mathcal{O}}(\max\{\sqrt{T}, T^ρ\})$. Core to our analysis is a novel framework for analyzing gradient-based algorithms for dueling bandit under corruption, and we demonstrate its general applicability by showing how this framework can be easily applied to obtain corruption-robust guarantees for other popular gradient-based dueling bandit algorithms. Our theoretical results are validated by extensive experiments.

Xuefeng Liu

We propose a rigorous method for computing two-sided eigenvalue bounds of the Schrödinger operator $H=-Δ+V$ with a confining potential on $\mathbb{R}^2$. The method combines domain truncation to a finite disk $D(R)$ on which the restricted eigenvalue problem is solved with a rigrous eigenvalue bound, where Liu's eigenvalue bound along with the Composite Enriched Crouzeix--Raviart (CECR) finite element method proposed plays a central role. Two concrete potentials are studied: the radially symmetric ring potential $V_1(x)=(|x|^2-1)^2$ and the Cartesian double-well $V_2(x)=(x_1^2-1)^2+x_2^2$. To author's knowledge, this paper reports the first rigorous eigenvalue bounds for Schrödinger operators on an unbounded domain.

Yan Zhang, Xuefeng Liu, Sipeng Chen et al.

Standard Bayesian Optimization (BO) assumes uniform smoothness across the search space an assumption violated in multi-regime problems such as molecular conformation search through distinct energy basins or drug discovery across heterogeneous molecular scaffolds. A single GP either oversmooths sharp transitions or hallucinates noise in smooth regions, yielding miscalibrated uncertainty. We propose RAMBO, a Dirichlet Process Mixture of Gaussian Processes that automatically discovers latent regimes during optimization, each modeled by an independent GP with locally-optimized hyperparameters. We derive collapsed Gibbs sampling that analytically marginalizes latent functions for efficient inference, and introduce adaptive concentration parameter scheduling for coarse-to-fine regime discovery. Our acquisition functions decompose uncertainty into intra-regime and inter-regime components. Experiments on synthetic benchmarks and real-world applications, including molecular conformer optimization, virtual screening for drug discovery, and fusion reactor design, demonstrate consistent improvements over state-of-the-art baselines on multi-regime objectives.

Guanghui Wang, Jinze Yu, Xing Zhang et al.

Large Language Models (LLMs) are increasingly deployed for structured data generation, yet output consistency remains critical for production applications. We introduce a comprehensive framework for evaluating and improving consistency in LLM-generated structured outputs. Our approach combines: (1) STED (Semantic Tree Edit Distance), a novel similarity metric balancing semantic flexibility with structural strictness when comparing JSON outputs, and (2) a consistency scoring framework aggregating multiple STED measurements across repeated generations to quantify reliability. Through systematic experiments on synthetic datasets with controlled schema, expression, and semantic variations, we demonstrate STED achieves superior performance ($0.86-0.90$ similarity for semantic equivalents, $0.0$ for structural breaks) compared to existing metrics including TED, BERTScore, and DeepDiff. Applying our framework to benchmark six LLMs reveals significant variations: Claude-3.7-Sonnet demonstrates exceptional consistency, maintaining near-perfect structural reliability even at high temperatures ($T=0.9$), while models like Claude-3-Haiku and Nova-Pro exhibit substantial degradation requiring careful tuning. Our framework enables practical applications including targeted model selection for structured tasks, iterative prompt refinement for reproducible results, and diagnostic analysis to identify inconsistency root causes. This work provides theoretical foundations and practical tools for ensuring reliable structured output generation in LLM-based production systems.

Wenkai Guo, Xuefeng Liu, Haolin Wang et al.

Fine-tuning large language models (LLMs) with local data is a widely adopted approach for organizations seeking to adapt LLMs to their specific domains. Given the shared characteristics in data across different organizations, the idea of collaboratively fine-tuning an LLM using data from multiple sources presents an appealing opportunity. However, organizations are often reluctant to share local data, making centralized fine-tuning impractical. Federated learning (FL), a privacy-preserving framework, enables clients to retain local data while sharing only model parameters for collaborative training, offering a potential solution. While fine-tuning LLMs on centralized datasets risks data leakage through next-token prediction, the iterative aggregation process in FL results in a global model that encapsulates generalized knowledge, which some believe protects client privacy. In this paper, however, we present contradictory findings through extensive experiments. We show that attackers can still extract training data from the global model, even using straightforward generation methods, with leakage increasing as the model size grows. Moreover, we introduce an enhanced attack strategy tailored to FL, which tracks global model updates during training to intensify privacy leakage. To mitigate these risks, we evaluate privacy-preserving techniques in FL, including differential privacy, regularization-constrained updates and adopting LLMs with safety alignment. Our results provide valuable insights and practical guidelines for reducing privacy risks when training LLMs with FL.

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.

Xinghao Wu, Jianwei Niu, Xuefeng Liu et al.

Federated Prototype Learning (FedPL) has emerged as an effective strategy for handling data heterogeneity in Federated Learning (FL). In FedPL, clients collaboratively construct a set of global feature centers (prototypes), and let local features align with these prototypes to mitigate the effects of data heterogeneity. The performance of FedPL highly depends on the quality of prototypes. Existing methods assume that larger inter-class distances among prototypes yield better performance, and thus design different methods to increase these distances. However, we observe that while these methods increase prototype distances to enhance class discrimination, they inevitably disrupt essential semantic relationships among classes, which are crucial for model generalization. This raises an important question: how to construct prototypes that inherently preserve semantic relationships among classes? Directly learning these relationships from limited and heterogeneous client data can be problematic in FL. Recently, the success of pre-trained language models (PLMs) demonstrates their ability to capture semantic relationships from vast textual corpora. Motivated by this, we propose FedTSP, a novel method that leverages PLMs to construct semantically enriched prototypes from the textual modality, enabling more effective collaboration in heterogeneous data settings. We first use a large language model (LLM) to generate fine-grained textual descriptions for each class, which are then processed by a PLM on the server to form textual prototypes. To address the modality gap between client image models and the PLM, we introduce trainable prompts, allowing prototypes to adapt better to client tasks. Extensive experiments demonstrate that FedTSP mitigates data heterogeneity while significantly accelerating convergence.

Guogang Zhu, Xuefeng Liu, Jianwei Niu et al.

It is often observed that the aggregated model in FL underperforms on local data until after several rounds of local training. This temporary performance drop can potentially slow down the convergence of the FL model. Prior work regards this performance drop as an inherent cost of knowledge sharing among clients and does not give it special attention. While some studies directly focus on designing techniques to alleviate the issue, its root causes remain poorly understood. To bridge this gap, we construct a framework that enables layer-peeled analysis of how feature representations evolve during model aggregation in FL. It focuses on two key aspects: (1) the intrinsic quality of extracted features, and (2) the alignment between features and their subsequent parameters -- both of which are critical to downstream performance. Using this framework, we first investigate how model aggregation affects internal feature extraction process. Our analysis reveals that aggregation degrades feature quality and weakens the coupling between intermediate features and subsequent layers, both of which are well shaped during local training. More importantly, this degradation is not confined to specific layers but progressively accumulates with network depth -- a phenomenon we term Cumulative Feature Degradation (CFD). CFD significantly impairs the quality of penultimate-layer features and weakens their coupling with the classifier, ultimately degrading model performance. We further revisit several widely adopted solutions through the lens of layer-peeled feature extraction to understand why they are effective in addressing aggregation-induced performance drop. Our results show that their effectiveness lies in mitigating the feature degradation described above, which is well aligned with our observations.

Pinxue Guo, Tony Huang, Peiyang He et al.

Open-vocabulary Video Instance Segmentation (OpenVIS) can simultaneously detect, segment, and track arbitrary object categories in a video, without being constrained to categories seen during training. In this work, we propose InstFormer, a carefully designed framework for the OpenVIS task that achieves powerful open-vocabulary capabilities through lightweight fine-tuning with limited-category data. InstFormer begins with the open-world mask proposal network, encouraged to propose all potential instance class-agnostic masks by the contrastive instance margin loss. Next, we introduce InstCLIP, adapted from pre-trained CLIP with Instance Guidance Attention, which encodes open-vocabulary instance tokens efficiently. These instance tokens not only enable open-vocabulary classification but also offer strong universal tracking capabilities. Furthermore, to prevent the tracking module from being constrained by the training data with limited categories, we propose the universal rollout association, which transforms the tracking problem into predicting the next frame's instance tracking token. The experimental results demonstrate the proposed InstFormer achieve state-of-the-art capabilities on a comprehensive OpenVIS evaluation benchmark, while also achieves competitive performance in fully supervised VIS task.

Zhengsu Chen, Jianwei Niu, Xuefeng Liu et al.

Convolutional neural networks (CNNs) have achieved remarkable success in image recognition. Although the internal patterns of the input images are effectively learned by the CNNs, these patterns only constitute a small proportion of useful patterns contained in the input images. This can be attributed to the fact that the CNNs will stop learning if the learned patterns are enough to make a correct classification. Network regularization methods like dropout and SpatialDropout can ease this problem. During training, they randomly drop the features. These dropout methods, in essence, change the patterns learned by the networks, and in turn, forces the networks to learn other patterns to make the correct classification. However, the above methods have an important drawback. Randomly dropping features is generally inefficient and can introduce unnecessary noise. To tackle this problem, we propose SelectScale. Instead of randomly dropping units, SelectScale selects the important features in networks and adjusts them during training. Using SelectScale, we improve the performance of CNNs on CIFAR and ImageNet.

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.

Yadu Babuji, Ben Blaiszik, Tom Brettin et al.

Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new drugs to counter the the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One promising approach is to train machine learning (ML) and artificial intelligence (AI) tools to screen large numbers of small molecules. As a contribution to that effort, we are aggregating numerous small molecules from a variety of sources, using high-performance computing (HPC) to computer diverse properties of those molecules, using the computed properties to train ML/AI models, and then using the resulting models for screening. In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. This data release encompasses structural information on the 4.2 B molecules and 60 TB of pre-computed data. Future releases will expand the data to include more detailed molecular simulations, computed models, and other products.

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.

Hao Su, Jianwei Niu, Xuefeng Liu et al.

Manga is a world popular comic form originated in Japan, which typically employs black-and-white stroke lines and geometric exaggeration to describe humans' appearances, poses, and actions. In this paper, we propose MangaGAN, the first method based on Generative Adversarial Network (GAN) for unpaired photo-to-manga translation. Inspired by how experienced manga artists draw manga, MangaGAN generates the geometric features of manga face by a designed GAN model and delicately translates each facial region into the manga domain by a tailored multi-GANs architecture. For training MangaGAN, we construct a new dataset collected from a popular manga work, containing manga facial features, landmarks, bodies, and so on. Moreover, to produce high-quality manga faces, we further propose a structural smoothing loss to smooth stroke-lines and avoid noisy pixels, and a similarity preserving module to improve the similarity between domains of photo and manga. Extensive experiments show that MangaGAN can produce high-quality manga faces which preserve both the facial similarity and a popular manga style, and outperforms other related state-of-the-art methods.